Bio-AlignIO-stockholm-1.7.3000755000765000024 013352276662 15577 5ustar00cjfieldsstaff000000000000Changes100644000765000024 35613352276662 17137 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3Summary of important user-visible changes for Bio-AlignIO-stockholm ------------------------------------------------------------------- 1.7.3 2018-09-24 19:13:36-05:00 America/Chicago * First release after split from bioperl-live. LICENSE100644000765000024 4414713352276662 16717 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3This software is copyright (c) 2018 by Peter Schattner , Chris Fields . This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. Terms of the Perl programming language system itself a) the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version, or b) the "Artistic License" --- The GNU General Public License, Version 1, February 1989 --- This software is Copyright (c) 2018 by Peter Schattner , Chris Fields . This is free software, licensed under: The GNU General Public License, Version 1, February 1989 GNU GENERAL PUBLIC LICENSE Version 1, February 1989 Copyright (C) 1989 Free Software Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The license agreements of most software companies try to keep users at the mercy of those companies. By contrast, our General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. The General Public License applies to the Free Software Foundation's software and to any other program whose authors commit to using it. You can use it for your programs, too. When we speak of free software, we are referring to freedom, not price. Specifically, the General Public License is designed to make sure that you have the freedom to give away or sell copies of free software, that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of a such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must tell them their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License Agreement applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any work containing the Program or a portion of it, either verbatim or with modifications. Each licensee is addressed as "you". 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this General Public License and to the absence of any warranty; and give any other recipients of the Program a copy of this General Public License along with the Program. You may charge a fee for the physical act of transferring a copy. 2. You may modify your copy or copies of the Program or any portion of it, and copy and distribute such modifications under the terms of Paragraph 1 above, provided that you also do the following: a) cause the modified files to carry prominent notices stating that you changed the files and the date of any change; and b) cause the whole of any work that you distribute or publish, that in whole or in part contains the Program or any part thereof, either with or without modifications, to be licensed at no charge to all third parties under the terms of this General Public License (except that you may choose to grant warranty protection to some or all third parties, at your option). c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the simplest and most usual way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this General Public License. d) You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 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BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 10. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS Appendix: How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to humanity, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) 19yy This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) 19xx name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (a program to direct compilers to make passes at assemblers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice That's all there is to it! --- The Artistic License 1.0 --- This software is Copyright (c) 2018 by Peter Schattner , Chris Fields . This is free software, licensed under: The Artistic License 1.0 The Artistic License Preamble The intent of this document is to state the conditions under which a Package may be copied, such that the Copyright Holder maintains some semblance of artistic control over the development of the package, while giving the users of the package the right to use and distribute the Package in a more-or-less customary fashion, plus the right to make reasonable modifications. 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It also means that recipients of the item may redistribute it under the same conditions they received it. 1. You may make and give away verbatim copies of the source form of the Standard Version of this Package without restriction, provided that you duplicate all of the original copyright notices and associated disclaimers. 2. You may apply bug fixes, portability fixes and other modifications derived from the Public Domain or from the Copyright Holder. A Package modified in such a way shall still be considered the Standard Version. 3. 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However, you may distribute this Package in aggregate with other (possibly commercial) programs as part of a larger (possibly commercial) software distribution provided that you do not advertise this Package as a product of your own. 6. The scripts and library files supplied as input to or produced as output from the programs of this Package do not automatically fall under the copyright of this Package, but belong to whomever generated them, and may be sold commercially, and may be aggregated with this Package. 7. C or perl subroutines supplied by you and linked into this Package shall not be considered part of this Package. 8. The name of the Copyright Holder may not be used to endorse or promote products derived from this software without specific prior written permission. 9. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. The End dist.ini100644000765000024 56213352276662 17307 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3name = Bio-AlignIO-stockholm version = 1.7.3 author = Peter Schattner author = Chris Fields copyright_holder = Peter Schattner , Chris Fields license = Perl_5 ;; Modules should be fixed so that these don't have to be removed. [@BioPerl] -remove = PodWeaver -remove = Test::NoTabs META.yml100644000765000024 1667713352276662 17172 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3--- abstract: 'stockholm sequence input/output stream' author: - 'Peter Schattner ' - 'Chris Fields ' build_requires: Bio::Root::Test: '0' File::Spec: '0' IO::Handle: '0' IPC::Open3: '0' Test::More: '0' lib: '0' perl: '5.006' warnings: '0' configure_requires: ExtUtils::MakeMaker: '0' dynamic_config: 0 generated_by: 'Dist::Zilla version 6.010, CPAN::Meta::Converter version 2.150010' license: perl meta-spec: url: http://module-build.sourceforge.net/META-spec-v1.4.html version: '1.4' name: Bio-AlignIO-stockholm requires: Bio::AlignIO: '0' Bio::AlignIO::Handler::GenericAlignHandler: '0' Bio::Index::Abstract: '0' Bio::Root::Root: '0' Bio::Seq::Meta: '0' Text::Wrap: '0' base: '0' strict: '0' resources: bugtracker: https://github.com/bioperl/bio-alignio-stockholm/issues homepage: https://metacpan.org/release/Bio-AlignIO-stockholm repository: git://github.com/bioperl/bio-alignio-stockholm.git version: 1.7.3 x_Dist_Zilla: perl: version: '5.026000' plugins: - class: Dist::Zilla::Plugin::GatherDir config: Dist::Zilla::Plugin::GatherDir: exclude_filename: [] exclude_match: [] follow_symlinks: 0 include_dotfiles: 0 prefix: '' prune_directory: [] root: . name: '@BioPerl/@Filter/GatherDir' version: '6.010' - class: Dist::Zilla::Plugin::PruneCruft name: '@BioPerl/@Filter/PruneCruft' version: '6.010' - class: Dist::Zilla::Plugin::ManifestSkip name: '@BioPerl/@Filter/ManifestSkip' version: '6.010' - class: Dist::Zilla::Plugin::MetaYAML name: '@BioPerl/@Filter/MetaYAML' version: '6.010' - class: Dist::Zilla::Plugin::License name: '@BioPerl/@Filter/License' version: '6.010' - class: Dist::Zilla::Plugin::ExtraTests name: '@BioPerl/@Filter/ExtraTests' version: '6.010' - class: Dist::Zilla::Plugin::ExecDir name: '@BioPerl/@Filter/ExecDir' version: '6.010' - class: Dist::Zilla::Plugin::ShareDir name: '@BioPerl/@Filter/ShareDir' version: '6.010' - class: Dist::Zilla::Plugin::MakeMaker config: Dist::Zilla::Role::TestRunner: default_jobs: 1 name: '@BioPerl/@Filter/MakeMaker' version: '6.010' - class: Dist::Zilla::Plugin::Manifest name: '@BioPerl/@Filter/Manifest' version: '6.010' - class: Dist::Zilla::Plugin::TestRelease name: '@BioPerl/@Filter/TestRelease' version: '6.010' - class: Dist::Zilla::Plugin::ConfirmRelease name: '@BioPerl/@Filter/ConfirmRelease' version: '6.010' - class: Dist::Zilla::Plugin::UploadToCPAN name: '@BioPerl/@Filter/UploadToCPAN' version: '6.010' - class: Dist::Zilla::Plugin::MetaConfig name: '@BioPerl/MetaConfig' version: '6.010' - class: Dist::Zilla::Plugin::MetaJSON name: '@BioPerl/MetaJSON' version: '6.010' - class: Dist::Zilla::Plugin::PkgVersion name: '@BioPerl/PkgVersion' version: '6.010' - class: Dist::Zilla::Plugin::PodSyntaxTests name: '@BioPerl/PodSyntaxTests' version: '6.010' - class: Dist::Zilla::Plugin::Test::Compile config: Dist::Zilla::Plugin::Test::Compile: bail_out_on_fail: '0' fail_on_warning: author fake_home: 0 filename: t/00-compile.t module_finder: - ':InstallModules' needs_display: 0 phase: test script_finder: - ':PerlExecFiles' skips: [] switch: [] name: '@BioPerl/Test::Compile' version: '2.057' - class: Dist::Zilla::Plugin::PodCoverageTests name: '@BioPerl/PodCoverageTests' version: '6.010' - class: Dist::Zilla::Plugin::MojibakeTests name: '@BioPerl/MojibakeTests' version: '0.8' - class: Dist::Zilla::Plugin::AutoPrereqs name: '@BioPerl/AutoPrereqs' version: '6.010' - class: Dist::Zilla::Plugin::AutoMetaResources name: '@BioPerl/AutoMetaResources' version: '1.21' - class: Dist::Zilla::Plugin::MetaResources name: '@BioPerl/MetaResources' version: '6.010' - class: Dist::Zilla::Plugin::Test::EOL config: Dist::Zilla::Plugin::Test::EOL: filename: xt/author/eol.t finder: - ':ExecFiles' - ':InstallModules' - ':TestFiles' trailing_whitespace: 1 name: '@BioPerl/Test::EOL' version: '0.19' - class: Dist::Zilla::Plugin::Encoding name: '@BioPerl/Encoding' version: '6.010' - class: Dist::Zilla::Plugin::NextRelease name: '@BioPerl/NextRelease' version: '6.010' - class: Dist::Zilla::Plugin::Git::Check config: Dist::Zilla::Plugin::Git::Check: untracked_files: die Dist::Zilla::Role::Git::DirtyFiles: allow_dirty: - Changes - dist.ini allow_dirty_match: [] changelog: Changes Dist::Zilla::Role::Git::Repo: git_version: 2.14.1 repo_root: . name: '@BioPerl/Git::Check' version: '2.042' - class: Dist::Zilla::Plugin::Git::Commit config: Dist::Zilla::Plugin::Git::Commit: add_files_in: [] commit_msg: v%v%n%n%c Dist::Zilla::Role::Git::DirtyFiles: allow_dirty: - Changes - dist.ini allow_dirty_match: [] changelog: Changes Dist::Zilla::Role::Git::Repo: git_version: 2.14.1 repo_root: . 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Dist::Zilla::Role::Git::StringFormatter: time_zone: local name: '@BioPerl/Git::Tag' version: '2.042' - class: Dist::Zilla::Plugin::FinderCode name: ':InstallModules' version: '6.010' - class: Dist::Zilla::Plugin::FinderCode name: ':IncModules' version: '6.010' - class: Dist::Zilla::Plugin::FinderCode name: ':TestFiles' version: '6.010' - class: Dist::Zilla::Plugin::FinderCode name: ':ExtraTestFiles' version: '6.010' - class: Dist::Zilla::Plugin::FinderCode name: ':ExecFiles' version: '6.010' - class: Dist::Zilla::Plugin::FinderCode name: ':PerlExecFiles' version: '6.010' - class: Dist::Zilla::Plugin::FinderCode name: ':ShareFiles' version: '6.010' - class: Dist::Zilla::Plugin::FinderCode name: ':MainModule' version: '6.010' - class: Dist::Zilla::Plugin::FinderCode name: ':AllFiles' version: '6.010' - class: Dist::Zilla::Plugin::FinderCode name: ':NoFiles' version: '6.010' zilla: class: Dist::Zilla::Dist::Builder config: is_trial: '0' version: '6.010' x_serialization_backend: 'YAML::Tiny version 1.70' MANIFEST100644000765000024 62513352276662 16774 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.010. Changes LICENSE MANIFEST META.json META.yml Makefile.PL dist.ini lib/Bio/AlignIO/stockholm.pm lib/Bio/Index/Stockholm.pm t/00-compile.t t/AlignIO.t t/Index.t t/author-eol.t t/author-mojibake.t t/author-pod-coverage.t t/author-pod-syntax.t t/data/pfam_tests.stk t/data/rfam_tests.stk t/data/testaln.stockholm t/data/tiny.stk t000755000765000024 013352276662 15763 5ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3Index.t100644000765000024 137113352276662 17361 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/t# -*-Perl-*- Test Harness script for Bioperl # $Id$ use strict; BEGIN { use lib '.'; use Bio::Root::Test; test_begin(-tests => 4); use_ok('Bio::Index::Stockholm'); } my $st_ind = Bio::Index::Stockholm->new(-filename => 'Wibbl6', -write_flag => 1, -verbose => 0); isa_ok $st_ind, 'Bio::Index::Stockholm'; $st_ind->make_index(test_input_file('testaln.stockholm')); ok ( -e "Wibbl6" ); my $aln = $st_ind->fetch_aln('PF00244'); isa_ok($aln,'Bio::SimpleAlign'); END { cleanup(); } sub cleanup { for my $root ( qw(Wibbl6) ) { unlink $root if( -e $root ); unlink "$root.pag" if( -e "$root.pag"); unlink "$root.dir" if( -e "$root.dir"); } } META.json100644000765000024 2736013352276662 17331 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3{ "abstract" : "stockholm sequence input/output stream", "author" : [ "Peter Schattner ", "Chris Fields " ], "dynamic_config" : 0, "generated_by" : "Dist::Zilla version 6.010, CPAN::Meta::Converter version 2.150010", "license" : [ "perl_5" ], "meta-spec" : { "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec", "version" : 2 }, "name" : "Bio-AlignIO-stockholm", "prereqs" : { "configure" : { "requires" : { "ExtUtils::MakeMaker" : "0" } }, "develop" : { "requires" : { "Pod::Coverage::TrustPod" : "0", "Test::EOL" : "0", "Test::Mojibake" : "0", "Test::More" : "0.88", "Test::Pod" : "1.41", "Test::Pod::Coverage" : "1.08" } }, "runtime" : { "requires" : { "Bio::AlignIO" : "0", 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0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/t# -*-Perl-*- Test Harness script for Bioperl use strict; BEGIN { use lib '.'; use Bio::Root::Test; test_begin(-tests => 87); use_ok('Bio::AlignIO::stockholm'); } my $DEBUG = test_debug(); my ($str,$aln,$strout,$status); # STOCKHOLM (multiple concatenated files) # Rfam $str = Bio::AlignIO->new( '-file' => test_input_file("rfam_tests.stk"), '-format' => 'stockholm'); $strout = Bio::AlignIO->new('-file' => ">".test_output_file(), '-format' => 'stockholm', ); isa_ok($str,'Bio::AlignIO'); $aln = $str->next_aln(); isa_ok($aln,'Bio::Align::AlignI'); is($aln->source, 'stockholm'); is($aln->get_seq_by_pos(1)->get_nse, 'Z11765.1/1-89'); is($aln->accession, 'RF00006'); is($aln->id, 'Vault'); is($aln->description,'Vault RNA'); # annotation my ($ann) = $aln->annotation->get_Annotations('alignment_comment'); isa_ok($ann, 'Bio::Annotation::Comment'); is($ann->text,'This family of RNAs are found as part of the enigmatic vault'. ' ribonucleoprotein complex. The complex consists of a major vault protein'. ' (MVP), two minor vault proteins (VPARP and TEP1), and several small '. 'untranslated RNA molecules. It has been suggested that the vault complex '. 'is involved in drug resistance. We have identified a putative novel vault '. 'RNA on chromosome 5 EMBL:AC005219.','Stockholm annotation'); is($ann->tagname,'alignment_comment','Stockholm annotation'); # test output $status = $strout->write_aln($aln); is $status, 1, "stockholm output test"; $aln = $str->next_aln(); isa_ok($aln,'Bio::Align::AlignI'); is($aln->source, 'stockholm'); is($aln->get_seq_by_pos(1)->get_nse, 'L43844.1/2-149'); is($aln->get_seq_by_pos(1)->version, '1'); is($aln->accession, 'RF00007'); is($aln->id, 'U12'); is($aln->description,'U12 minor spliceosomal RNA'); my @anns = $aln->annotation->get_Annotations('reference'); $ann = shift @anns; isa_ok($ann, 'Bio::Annotation::Reference', 'Stockholm annotation'); $ann = shift @anns; is($ann->pubmed,'9149533', 'Stockholm annotation'); is($ann->title, 'Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge.', 'Stockholm annotation'); is($ann->authors,'Tarn WY, Steitz JA;', 'Stockholm annotation'); is($ann->location,'Trends Biochem Sci 1997;22:132-137.', 'Stockholm annotation'); # alignment meta data my $meta = $aln->consensus_meta; isa_ok($meta, 'Bio::Seq::MetaI'); my ($name) = $meta->meta_names; is($name,'SS_cons', 'Rfam meta data'); my $meta_str = $meta->named_meta($name); is($meta_str, '...<<<<<..........>>>>>........<<<<......<<<<......>>>>>>>>'. '<<<<<.......>>>>>...........<<<<<<<...<<<<<<<.....>>>>>>>.>>>>>>>..<<<'. '<<<<<<.........>>>>>>>>>...', 'Rfam meta data'); $aln = $str->next_aln(); is($aln->source, 'stockholm'); isa_ok($aln,'Bio::Align::AlignI'); is($aln->get_seq_by_pos(1)->get_nse, 'AJ295015.1/58-1'); is($aln->get_seq_by_pos(1)->strand, -1); is($aln->accession, 'RF00008'); is($aln->id, 'Hammerhead_3'); is($aln->description,'Hammerhead ribozyme (type III)'); # alignment meta data $meta = $aln->consensus_meta; isa_ok($meta, 'Bio::Seq::MetaI'); ($name) = $meta->meta_names; is($name,'SS_cons', 'Rfam meta data'); $meta_str = $meta->named_meta($name); is($meta_str, '.<<<<<<..<<<<<.........>>>>>.......<<<<.....................'. '...........>>>>...>>>>>>.', 'Rfam meta data'); # STOCKHOLM (Pfam) $str = Bio::AlignIO->new( '-file' => test_input_file("pfam_tests.stk"), '-format' => 'stockholm'); isa_ok($str,'Bio::AlignIO'); $aln = $str->next_aln(); is($aln->source, 'stockholm'); isa_ok($aln,'Bio::Align::AlignI'); is($aln->get_seq_by_pos(1)->get_nse, 'RAD25_SCHPO/5-240'); is($aln->accession, 'PF00244.9'); is($aln->id, '14-3-3'); is($aln->description,'14-3-3 protein'); ($ann) = $aln->annotation->get_Annotations('gathering_threshold'); isa_ok($ann, 'Bio::Annotation::SimpleValue'); is($ann->display_text, '25.00 25.00; 25.00 25.00;', 'Pfam annotation'); $aln = $str->next_aln(); is($aln->source, 'stockholm'); isa_ok($aln,'Bio::Align::AlignI'); is($aln->get_seq_by_pos(1)->get_nse, 'COMB_CLOAB/6-235'); is($aln->accession, 'PF04029.4'); is($aln->id, '2-ph_phosp'); is($aln->description,'2-phosphosulpholactate phosphatase'); $aln = $str->next_aln(); isa_ok($aln,'Bio::Align::AlignI'); is($aln->source, 'stockholm'); is($aln->get_seq_by_pos(1)->get_nse, 'Y278_HAEIN/174-219'); is($aln->accession, 'PF03475.3'); is($aln->id, '3-alpha'); is($aln->description,'3-alpha domain'); # alignment meta data $meta = $aln->consensus_meta; isa_ok($meta, 'Bio::Seq::MetaI'); my %test_data = ('SA_cons' => '6000320010013274....3372052026033.108303630350385563', 'SS_cons' => 'SCBHHHHHHHHHTSCC....CHHHHHHHHTSTT.CCHHHHHHHHHHHHHSSC', 'seq_cons' => 'plTVtclsclhasc......stphLcphLshss.Lupsa+cohpK+lspshs',); for my $name ($meta->meta_names) { ok(exists $test_data{$name}, 'Pfam aln meta data'); $meta_str = $meta->named_meta($name); is($meta_str, $test_data{$name}, 'Pfam aln meta data'); } %test_data = (); # sequence meta data %test_data = ('SA' => '6000320010013274....3372052026033.108303630350385563', 'SS' => 'SCBHHHHHHHHHTSCC....CHHHHHHHHTSTT.CCHHHHHHHHHHHHHSSC'); for my $seq ($aln->each_seq) { for my $name ($seq->meta_names) { ok(exists $test_data{$name}, 'Pfam seq meta data'); is($seq->named_meta($name), $test_data{$name}, 'Pfam seq meta data'); } } # sequence-specific alignments # these are generally DBLinks. However, simple DBLinks are not RangeI, so these # are now Target (which now is-a DBLink). Since these are per-seq, these are # stored in a full-length SeqFeature as annotation. For now only sequences which # have this annotation have a SeqFeature. my @feats = $aln->get_SeqFeatures; is(scalar(@feats),6); isa_ok($feats[0], 'Bio::SeqFeatureI'); isa_ok($feats[0]->entire_seq, 'Bio::Seq::Meta'); my ($link) = $feats[0]->annotation->get_Annotations('dblink'); isa_ok($link, 'Bio::AnnotationI'); isa_ok($link, 'Bio::Annotation::DBLink'); is($link->database, 'PDB'); is($link->start, '178'); is($link->end, '224'); is($link->primary_id, '1o65'); is($link->target_id, '1o65'); # if not set, defaults to primary_id is($link->optional_id, 'A'); ($link) = $feats[3]->annotation->get_Annotations('dblink'); is($link->database, 'PDB'); is($link->start, '178'); is($link->end, '224'); is($link->target_id, '1o67'); # bug #3420 my $in = Bio::AlignIO->new(-file => test_input_file('tiny.stk'), -format => 'stockholm'); $aln = $in->next_aln; is($aln->id, 'NoName'); is($aln->get_seq_by_id('a')->display_id, 'a'); is($aln->get_seq_by_id('b')->display_id, 'b'); Makefile.PL100644000765000024 333013352276662 17631 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3# This file was automatically generated by Dist::Zilla::Plugin::MakeMaker v6.010. use strict; use warnings; use 5.006; use ExtUtils::MakeMaker; my %WriteMakefileArgs = ( "ABSTRACT" => "stockholm sequence input/output stream", "AUTHOR" => "Peter Schattner , Chris Fields ", "CONFIGURE_REQUIRES" => { "ExtUtils::MakeMaker" => 0 }, "DISTNAME" => "Bio-AlignIO-stockholm", "LICENSE" => "perl", "MIN_PERL_VERSION" => "5.006", "NAME" => "Bio::AlignIO::stockholm", "PREREQ_PM" => { "Bio::AlignIO" => 0, "Bio::AlignIO::Handler::GenericAlignHandler" => 0, "Bio::Index::Abstract" => 0, "Bio::Root::Root" => 0, "Bio::Seq::Meta" => 0, "Text::Wrap" => 0, "base" => 0, "strict" => 0 }, "TEST_REQUIRES" => { "Bio::Root::Test" => 0, "File::Spec" => 0, "IO::Handle" => 0, "IPC::Open3" => 0, "Test::More" => 0, "lib" => 0, "warnings" => 0 }, "VERSION" => "1.7.3", "test" => { "TESTS" => "t/*.t" } ); my %FallbackPrereqs = ( "Bio::AlignIO" => 0, "Bio::AlignIO::Handler::GenericAlignHandler" => 0, "Bio::Index::Abstract" => 0, "Bio::Root::Root" => 0, "Bio::Root::Test" => 0, "Bio::Seq::Meta" => 0, "File::Spec" => 0, "IO::Handle" => 0, "IPC::Open3" => 0, "Test::More" => 0, "Text::Wrap" => 0, "base" => 0, "lib" => 0, "strict" => 0, "warnings" => 0 ); unless ( eval { ExtUtils::MakeMaker->VERSION(6.63_03) } ) { delete $WriteMakefileArgs{TEST_REQUIRES}; delete $WriteMakefileArgs{BUILD_REQUIRES}; $WriteMakefileArgs{PREREQ_PM} = \%FallbackPrereqs; } delete $WriteMakefileArgs{CONFIGURE_REQUIRES} unless eval { ExtUtils::MakeMaker->VERSION(6.52) }; WriteMakefile(%WriteMakefileArgs); 00-compile.t100644000765000024 270413352276662 20160 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/tuse 5.006; use strict; use warnings; # this test was generated with Dist::Zilla::Plugin::Test::Compile 2.057 use Test::More; plan tests => 2 + ($ENV{AUTHOR_TESTING} ? 1 : 0); my @module_files = ( 'Bio/AlignIO/stockholm.pm', 'Bio/Index/Stockholm.pm' ); # no fake home requested my @switches = ( -d 'blib' ? '-Mblib' : '-Ilib', ); use File::Spec; use IPC::Open3; use IO::Handle; open my $stdin, '<', File::Spec->devnull or die "can't open devnull: $!"; my @warnings; for my $lib (@module_files) { # see L my $stderr = IO::Handle->new; diag('Running: ', join(', ', map { my $str = $_; $str =~ s/'/\\'/g; q{'} . $str . q{'} } $^X, @switches, '-e', "require q[$lib]")) if $ENV{PERL_COMPILE_TEST_DEBUG}; my $pid = open3($stdin, '>&STDERR', $stderr, $^X, @switches, '-e', "require q[$lib]"); binmode $stderr, ':crlf' if $^O eq 'MSWin32'; my @_warnings = <$stderr>; waitpid($pid, 0); is($?, 0, "$lib loaded ok"); shift @_warnings if @_warnings and $_warnings[0] =~ /^Using .*\bblib/ and not eval { +require blib; blib->VERSION('1.01') }; if (@_warnings) { warn @_warnings; push @warnings, @_warnings; } } is(scalar(@warnings), 0, 'no warnings found') or diag 'got warnings: ', ( Test::More->can('explain') ? Test::More::explain(\@warnings) : join("\n", '', @warnings) ) if $ENV{AUTHOR_TESTING}; author-eol.t100644000765000024 112013352276662 20361 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/t BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } use strict; use warnings; # this test was generated with Dist::Zilla::Plugin::Test::EOL 0.19 use Test::More 0.88; use Test::EOL; my @files = ( 'lib/Bio/AlignIO/stockholm.pm', 'lib/Bio/Index/Stockholm.pm', 't/00-compile.t', 't/AlignIO.t', 't/Index.t', 't/author-eol.t', 't/author-mojibake.t', 't/author-pod-coverage.t', 't/author-pod-syntax.t' ); eol_unix_ok($_, { trailing_whitespace => 1 }) foreach @files; done_testing; data000755000765000024 013352276662 16674 5ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/ttiny.stk100644000765000024 15513352276662 20523 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/t/data# STOCKHOLM 1.0 #=GF AU HMMER 2.3.2 a SEQENCEQQQQQ b PRTEINAACIDQ #=GC RF xxxxxxxxxxxx // author-mojibake.t100644000765000024 35313352276662 21352 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/t#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } use strict; use warnings qw(all); use Test::More; use Test::Mojibake; all_files_encoding_ok(); rfam_tests.stk100644000765000024 5400613352276662 21753 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/t/data# STOCKHOLM 1.0 #=GF AC RF00006 #=GF ID Vault #=GF DE Vault RNA #=GF AU Bateman A #=GF SE Bateman A #=GF SS Predicted; PFOLD; Bateman A #=GF GA 25.00 #=GF TC 41.33 #=GF NC 23.46 #=GF TP Gene; #=GF BM cmbuild CM SEED #=GF BM cmsearch --local -W 150 CM SEQDB #=GF DR URL; http://vaults.arc.ucla.edu/sci/sci_home.htm; #=GF CC This family of RNAs are found as part of the enigmatic vault #=GF CC ribonucleoprotein complex. The complex consists of a major #=GF CC vault protein (MVP), two minor vault proteins (VPARP and TEP1), #=GF CC and several small untranslated RNA molecules. It has been #=GF CC suggested that the vault complex is involved in drug #=GF CC resistance. #=GF CC We have identified a putative novel vault RNA on chromosome 5 #=GF CC EMBL:AC005219. #=GF SQ 11 Z11765.1/1-89 GGUCAGCAACAGCUC.AGCGGUUACUUCUCGA.....CACGGAAUUGUAA AF210457.1/105-240 GGCCAGCUUUAGCUC.AGCGGUUAC..UUCGACAGUGGUUCAGUUCAU.U AY007237.1/1-136 GGCCAGCUUUAGCUG.AGCGGUUAC..UUUGACAGUGUUUCAGUUCAU.U Z11771.1/1-137 GGCCAGCUUUAGCUC.AGCGGUUAC..UUCGACGUGCUCCAGUUUGAGCA AC116353.2/181870-181951 GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGCGUGU.............C AF058927.1/1-92 GGYCAGCUUYAGCUC.AGCGGUUAC..UUCGACAGUUCUUUAAUUG...A AC005219.1/49915-50008 GGUCGGAGUUAGCUCAAGCGGUUAC..CUCCUCAUGCC...........G AF058926.1/1-82 GGYCAGCWWYAGCUC.AGCGGUUAC..UUCGAGUAC.............A AC116353.2/174637-174718 GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGAGUAC.............A AC116353.2/166987-167078 GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGACAGUUCUUUAAUUG...A Z97054.1/58392-58486 GGCUGGCUUUAGCUC.AGCGGUUAC..UUCGACAAUGCUUUCCAUGGUUA #=GC SS_cons .<<<<<.....<<<<..<<<<.......<<<<.................. Z11765.1/1-89 UUCUG........................AAAACCUUUC........... AF210457.1/105-240 ACCAGCUAUUCGUAGCAGGUUCGAACAACACAACCAACCACUUACCUAAC AY007237.1/1-136 ACCAGCUAUUCGUAGCAGGUUCAAAUAACACAACCAACCACUUGCCUAAC Z11771.1/1-137 GGCUAUGUAACGUGGUCGGUUCGAGCAACACAACCAGCCGCUUGCCUAUC AC116353.2/181870-181951 AUCAA........................ACCACCUCUC........... AF058927.1/1-92 AACAA........................GCAACCUGUC........... AC005219.1/49915-50008 GACUU........................UCUAUCUGUCCAUCUCUGU.. AF058926.1/1-82 UUGUA........................ACCACCUCUC........... AC116353.2/174637-174718 UUGUA........................ACCACCUCUC........... AC116353.2/166987-167078 AACAA........................GCAACCUGUC........... Z97054.1/58392-58486 GGAAA........................CCAACCUCUC........... #=GC SS_cons ................................<<<............... Z11765.1/1-89 ..........GGGGUUCGAAACCCGCGGGCGCCACCUGAC AF210457.1/105-240 CCGUGAGUGUUUGGUUCGAGACCCGCGGGCGCUCCCUGGC AY007237.1/1-136 CCAUGAGUGUUUGGUUCGAGACCGGCGGGCGCUCCCUGGC Z11771.1/1-137 UGGUGAGUGGUUGGUUCGAGACCCGCGGGCGCUCUCUGGC AC116353.2/181870-181951 .......UGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGC AF058927.1/1-92 .......UGGGUGGUUCGARACCCGCGGCCGCUMYCUGGC AC005219.1/49915-50008 .......GCUGGGGUUCGAGACCCGCGGGUGCUUACUGAC AF058926.1/1-82 .......UGGGUGGUUCGARACCCGCGGSCGCYMYCUGRC AC116353.2/174637-174718 .......UGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGC AC116353.2/166987-167078 .......UGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGU Z97054.1/58392-58486 .......UGGGUGGUUUGAGACCCGUGGGCCCUCUCCAGU #=GC SS_cons ............>>>>>>>...>>>>>>>>.....>>>>> // # STOCKHOLM 1.0 #=GF AC RF00007 #=GF ID U12 #=GF DE U12 minor spliceosomal RNA #=GF AU Griffiths-Jones SR, Mifsud W #=GF SE Shukla GC and Padgett RA, PMID:10199569 #=GF SS Published; PMID:10199569 #=GF GA 10.00 #=GF TC 11.43 #=GF NC undefined #=GF TP Gene; snRNA; splicing; #=GF BM cmbuild CM SEED #=GF BM cmsearch -W 160 CM SEQDB #=GF RN [1] #=GF RM 10199569 #=GF RT Conservation of functional features of U6atac and U12 snRNAs between #=GF RT vertebrates and higher plants. #=GF RA Shukla GC, Padgett RA; #=GF RL RNA 1999;5:525-538. #=GF RN [2] #=GF RM 9149533 #=GF RT Pre-mRNA splicing: the discovery of a new spliceosome doubles the #=GF RT challenge. #=GF RA Tarn WY, Steitz JA; #=GF RL Trends Biochem Sci 1997;22:132-137. #=GF RN [3] #=GF RM 11864616 #=GF RT The divergent U12-type spliceosome is required for pre-mRNA splicing #=GF RT and is essential for development in Drosophila. #=GF RA Otake LR, Scamborova P, Hashimoto C, Steitz JA; #=GF RL Mol Cell 2002;9:439-446. #=GF CC The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, #=GF CC and U11 snRNAs and associated proteins, forms a spliceosome that #=GF CC cleaves a divergent class of low-abundance pre-mRNA introns. #=GF CC Although the U12 sequence is very divergent from that of U2 #=GF CC (Rfam:RF00004), the two are functionally analogous [2]. #=GF SQ 7 L43844.1/2-149 .UGCCUUAAACUUAUGAGUAAGGAAAAUAACAACU......CGGGGUGAC L43843.1/2-150 .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC L43846.1/332-460 .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC L43845.1/357-512 AUGUCUUAAACUUAUGAGUAAGGAAAAUAACGAUUGUUAUUCGGGGUGAU J04119.1/2-130 .UGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC Z93241.11/76641-76790 AUGCCUUAAACUUAUGAGUAAGGAAAAUAACGAUU......CGGGGUGAC AL513366.11/57716-57871 AUGUCUUAAACUUAUGAGUAAGGAAAAUAACGAUUGUUAUUCGGGGUGAU #=GC SS_cons ...<<<<<..........>>>>>........<<<<......<<<<..... L43844.1/2-149 GCCCGAGUCCUCACUACUGAUGUGAGAGGAAUUUUUGUGCGGGUACAGGU L43843.1/2-150 GCCCGAGUCCUCACUGCUUAUGUGAGAAGAAUUUUUGAGCGGGUAUAGGU L43846.1/332-460 GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU L43845.1/357-512 GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCUGGUAAAGGU J04119.1/2-130 GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU Z93241.11/76641-76790 GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCGGGUAAAGGU AL513366.11/57716-57871 GCCCGAAUCCUCACUGCUAAUGUGAGACGAAUUUUUGAGCUGGUAAAGGU #=GC SS_cons .>>>>>>>><<<<<.......>>>>>...........<<<<<<<...<<< L43844.1/2-149 CGUCCCC.GGGUGACCCGCUUACUUCGCGGGAUGCCCAGGUGCAAUGAUC L43843.1/2-150 UGCAAUCUGAGCGACCCGCCUACUUUGCGGGAUGCCUGGGUGACGCGAUC L43846.1/332-460 CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCC.............. L43845.1/357-512 CGCCCCUAAGGUGACCAGCCUACUUUGCGGGAUGCCUAGGAGUCGCGAUC J04119.1/2-130 CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCC.............. Z93241.11/76641-76790 CGCCCUCAAGGUGACCCGCCUACUUUGCGGGAUGCCUGGGAGUUGCGAUC AL513366.11/57716-57871 CGCCCCUAAGGUGACCAGCCUACUUUGCGGGAUGCCUAGGAGUCGCGAUC #=GC SS_cons <<<<.....>>>>>>>.>>>>>>>..<<<<<<<<<.........>>>>>> L43844.1/2-149 UGCCCG L43843.1/2-150 UGCCCG L43846.1/332-460 ...... L43845.1/357-512 UGCCUG J04119.1/2-130 ...... Z93241.11/76641-76790 UGCCCG AL513366.11/57716-57871 UGCCUG #=GC SS_cons >>>... // # STOCKHOLM 1.0 #=GF AC RF00008 #=GF ID Hammerhead_3 #=GF DE Hammerhead ribozyme (type III) #=GF AU Bateman A #=GF SE Bateman A #=GF SS Published; PMID:7969422 #=GF GA 29.00 #=GF TC 29.53 #=GF NC 28.96 #=GF TP Gene; ribozyme; #=GF BM cmbuild CM SEED #=GF BM cmsearch -W 130 CM SEQDB #=GF RN [1] #=GF RM 7969422 #=GF RT Three-dimensional structure of a hammerhead ribozyme. #=GF RA Pley HW, Flaherty KM, McKay DB; #=GF RL Nature 1994;372:68-74. #=GF RN [2] #=GF RM 9506521 #=GF RT The structural basis of hammerhead ribozyme self-cleavage. #=GF RA Murray JB, Terwey DP, Maloney L, Karpeisky A, Usman N, Beigelman L, #=GF RA Scott WG; #=GF RL Cell 1998;92:665-673. #=GF RN [3] #=GF RM 10899150 #=GF RT Distribution of hammerhead and hammerhead-like RNA motifs through the #=GF RT GenBank. #=GF RA Ferbeyre G, Bourdeau V, Pageau M, Miramontes P, Cedergren R; #=GF RL Genome Res 2000;10:1011-1019. #=GF CC The hammerhead ribozyme is one of the smallest catalytic #=GF CC RNAs. These RNAs have an endonuclease function, and most #=GF CC often are autocatalytic. Structurally it is composed of #=GF CC three base paired helices, separated by short linkers of #=GF CC conserved sequence. These helices are called I, II and III. #=GF CC We have classified hammerhead ribozymes into three types #=GF CC based on which helix the 5' and 3' ends of the sequence #=GF CC join. This family are the type III hammerheads. #=GF CC The conserved uridine-turn links helix I #=GF CC to helix II and usually has the sequence CUGA. Helix II and #=GF CC III are linked by a sequence CGAAA. The cleavage reaction #=GF CC occurs between helix III and I, and is usually a C. #=GF CC Hammerhead ribozymes are found in plant viroids and other #=GF CC small replicating sattelite RNA species. Hammerhead #=GF CC ribozymes have been found in animals as well as plants. #=GF CC This family includes a couple of false matches currently #=GF CC these are EMBL:AC078923 and EMBL:BC050488. These animal #=GF CC sequences are not expected to be hammerhead ribozymes. #=GF SQ 84 AJ295015.1/58-1 ACAGAGUC.UGACAAA......CCGUCACUGAAGACGUUCAACUU..... AJ295018.1/58-1 ACAGGGUC.UGACAAA......CCGUCACUGAAGACGUUCAACUU..... AJ536620.1/206-152 CCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCAA......... AJ536615.1/1-44 .........GGGUGGUG.UGUACCAUCCCUGAUGAGUCCAA......... AJ536612.1/206-152 UCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCGA......... AJ536617.1/1-40 .........GGGUGGUGUGUA.CCACCCCUGAUGAGUCCGA......... AJ536614.1/206-152 UCACCGUC.GGAAAGUG.UGCGCUUUCCCUGAUGAGCCCAA......... AJ536620.1/1-40 .........GGGUGGUGUGUG.CCACCCCUGAUGAGUCCGA......... AJ536619.1/206-152 CCACCGUC.GGAAAGUG.UGUACUUUCCCUGAUGAGUCCGA......... AJ550911.1/56-3 CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGUUGCUGA....... AF170503.1/280-333 GAAAGGUC.UGUGCUU......AGCACACUGACGAGUUCCUGA....... AF170504.1/284-337 GAUAAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA....... AJ550912.1/56-3 CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGUUGCUGA....... AJ247113.1/134-53 .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC AJ241833.1/282-334 AAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA....... AJ241841.1/57-3 CAAAAGUU.UGGGCUAA.....AGCCCACUGAUGAGCCGCUGA....... AJ241839.1/282-334 GAUGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA....... AJ550901.1/282-334 GAAGAGUC..GCGCUA......AGCGCACUGAUGAGUCUUUGA....... AJ005298.1/56-3 CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA....... AJ241819.1/56-3 CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA....... AJ005320.1/281-333 GAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA....... AJ005310.1/56-3 CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA....... AF339740.1/56-3 CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGCCGUUGA....... AJ241828.1/56-3 CAUAAGUC.UGGGUUA......AGCCCACUGAUGAGCCGUUGA....... AJ550906.1/56-3 CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGUCGCUGC....... AJ550903.1/281-333 GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA....... AJ241831.1/56-3 CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA....... AJ241840.1/56-3 CAGAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA....... AJ005303.1/56-3 CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA....... AJ005312.1/56-3 CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA....... AJ550906.1/282-334 GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA....... AJ550907.1/56-3 CAUAAGUC.UGGGCUU......AGCCUACUGAUGAGUCGCUGC....... AF170503.1/55-3 CAUAAGUC.UGGGCUU......AG.CCACUGACGAGUCGCUGG....... Y14700.1/133-53 .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGAUGAGGCUGUGGAGAGAGC AJ005321.1/281-333 GAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA....... AJ241845.1/282-335 GAUGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA....... AJ005322.1/56-3 CAUAAGUC.UGGGCUA......AGCCCACUGACGAGCCGUUGA....... M83545.1/56-3 CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGUCGCUGA....... AJ005305.1/56-3 CAAAAGUC.UGGGCUA......AGCCCACUGACGAGCCGCUGG....... AJ550908.1/281-334 GAAGAGUC.UGCGCUU......AGCGCACUCAUGAGUCUCUGA....... AJ550909.1/56-3 CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGUUGCUGC....... AJ241843.1/56-3 CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGCCACUGA....... AF170523.1/55-3 CAAAAGUC.UGGGCUU......AG.CCACUGAUGAGCCGUUGA....... AF170509.1/56-3 CAUAAGUC.UAGGCUU......AGCCCACUGAUGAGCCGUUGA....... AJ241847.1/281-334 GAAGAGUC.UGUGCUA......AGCACACUGAUGAGUUUCUGA....... AJ241823.1/282-335 AAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUAA....... AJ247122.1/132-52 .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC AJ005300.1/282-335 UAAGAGUC.UGUGGUA......AGCACACUGAUGAGUCUCUGA....... AJ005302.1/281-334 AAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA....... AJ005318.1/56-3 CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA....... AF339739.1/56-3 CAUAAGUC.UGGGCUU......AGCCCACUGAUGAGGCGUUGA....... AJ241838.1/56-3 CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCUGCUGA....... AJ247121.1/133-53 .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGC AJ550911.1/282-335 GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA....... AJ550898.1/282-335 GAAGAGUC.UGCGCUA......AGCGCACUGAUGAGUCUUUGA....... AF170516.1/283-335 GAAGAGUC..GUGCUU......AGCACACUGAUGAGUCUCUGA....... AJ005319.1/56-3 CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGUUGA....... AJ550899.1/56-3 CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCUUUGC....... AF170519.1/55-3 CAUAAGUC.UGGGCUU......AG.CCACUGAUGAGCCGUUGA....... AJ247116.1/133-53 .UCCAGUC.GAGACCUGAAGUGGGUUUACUGAUGAGGCUGUGGAGAGAGC AJ550907.1/281-333 AAAGAGUC..GCGCUU......AGCGCACUGAUGAGUCUCUGA....... AJ241850.1/282-334 UAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA....... AF170499.1/56-3 CAAAAGUC.UGGGCUA......AGCCCACUGAUGAGCCGCUGA....... AF170520.1/282-335 GAUAAGUC.UGUGCUU......AGCACACUGAUGAGUCUCUGA....... AJ005299.1/282-335 UAAGAGUC.UGUGCUA......AGCACACUGAUGAAUCUCUGA....... AJ005312.1/282-335 GAUGAGUC.UGUGCUA......AGCACACUGAUGAGUCUAUGA....... AJ550909.1/282-333 GAAGAGUC..GCGCUU......AGCGCACUGAUGAGUCUCUGA....... AJ005322.1/281-334 GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA....... AJ005294.1/282-334 UAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA....... AJ247123.1/132-52 .UCCAGUC.GAGACCUGAAGUGGGUUUCCUGAUGAGGCUGUGGAGAGAGC AJ550900.1/56-3 CAUAAGUC.UGGGCUA......AGCCCACUGAUGAGCCUUUGC....... AJ241830.1/282-334 AAAGAGUC..GUGCUA......AGCACACUGAUGAGUCUCUGA....... AJ241831.1/281-334 GAAGAGUC.UGUGCUA......AGCACACUGAUGAGUCUCUGA....... M83545.1/282-335 GAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA....... AJ550910.1/282-336 GAAGAGUCCUGCGCUU......AGCGCACUGACGAGUCUCUGA....... AJ005314.1/281-334 AAAGAGUC.UGUGCUA......AGCACACUGACGAGUCUCUGA....... Y12833.1/339-285 CCGCUAUA.UGGGGAUGUGUG.UCCCUACUGACGAGUUCAA......... M63666.1/246-192 CCGGUGUC.UCAAGGUGCGUA.CCUUGACUGAUGAGUCCGA......... J02439.1/42-95 UGUCCGUA..GUGGAUGUGUA.UCCACUCUGAUGAGUCCGA......... J02386.1/42-95 UGUCCGUA..GUGGAUGUGUA.UCCACUCUGAUGAGUCCAA......... M33000.1/55-110 ACGCUGUC.UGUACUUGUAUC.AGUACACUGACGAGUCCCU......... M33001.1/56-111 ACGCUGUC.UGUACUUAUAUC.AGUACACUGACGAGUCCCU......... D00685.1/1-46 .........GCCAGACGU.GGACCCGGCCUGAUGAGUCCGAAA....... M17439.1/1-48 .........ACCGGAUGUGCUUUCCGGUCUGAUGAGUCCGU......... #=GC SS_cons .<<<<<<..<<<<<.........>>>>>.......<<<<........... AJ295015.1/58-1 ...............GCGUUGAACAGAAACUCUGC AJ295018.1/58-1 ...............GCGUUGAACAGAAACUCUGC AJ536620.1/206-152 ...................AAGGGCGAAACGGUAC AJ536615.1/1-44 ...................AAGGACGAAAUGG... AJ536612.1/206-152 ...................AAGGGCGAAACGGUAC AJ536617.1/1-40 ...................AAGGACGAA....... AJ536614.1/206-152 ...................AAGGGCGAAACGGUAC AJ536620.1/1-40 ...................AAGGACGAA....... AJ536619.1/206-152 ...................AAGGACGAAACGGUAC AJ550911.1/56-3 .................AACGCAACGAAACUUUUG AF170503.1/280-333 .................AAUGGAACGAAACCUUUU AF170504.1/284-337 .................AAUGAGACGAAACUUAUC AJ550912.1/56-3 .................GAUGCGACGAAACUUUUG AJ247113.1/134-53 AAAUUGCUUUACUCCCGCACAAGCCGAAACUGGA. AJ241833.1/282-334 .................AAUGAGACGAAACUCUUU AJ241841.1/57-3 .................AAUGCGGCGAAACUUUUG AJ241839.1/282-334 .................AAUGAGACGAAACUCAUA AJ550901.1/282-334 .................GAUAAGACGAAACUCUUC AJ005298.1/56-3 .................GAUACGGCGAAACUUUUG AJ241819.1/56-3 .................AAUACGGCGAAACUUUUG AJ005320.1/281-333 .................AAUGAGACGAAACUCUUU AJ005310.1/56-3 .................AAUGCGGCGAAACUUUUG AF339740.1/56-3 .................GAUACGGCGGAACUUAUG AJ241828.1/56-3 .................GAUACGGCGAAACUUAUG AJ550906.1/56-3 .................GAUGCGACGAAACUUAUG AJ550903.1/281-333 .................AAUGAGACGAAACUCUUU AJ241831.1/56-3 .................GAUACGGCGAAACUUCUG AJ241840.1/56-3 .................AAUGCGGCGAAACUUUUG AJ005303.1/56-3 .................GAUACGGCGAAACUUUUG AJ005312.1/56-3 .................AAUGCGGCUAAACUUUUG AJ550906.1/282-334 .................GAUGAGACGAAACUCUUC AJ550907.1/56-3 .................GAUGCGACGAAACUUAUG AF170503.1/55-3 .................GAUACGGCGAAACUUAUG Y14700.1/133-53 GAAAGCUUUACUCCCA.CACAAGCCGAAACUGGA. AJ005321.1/281-333 .................AAUGAGACGAAACUCUUG AJ241845.1/282-335 .................AAUGAGACGAAACUCAUG AJ005322.1/56-3 .................GAUACGGCGAAACUUAUG M83545.1/56-3 .................AAUGCGACGAAACUUAUG AJ005305.1/56-3 .................GAUACGGCGAAACUUUUG AJ550908.1/281-334 .................GAUGAGACGAAACUCUUC AJ550909.1/56-3 .................GAUGCAACGAAACUUAUG AJ241843.1/56-3 .................AAUGCGGCGAAACUUUUG AF170523.1/55-3 .................GAUACGGCGAAACUUUUG AF170509.1/56-3 .................GAUACGGCGAAACUUAUG AJ241847.1/281-334 .................AAUGAGACGAAACUCUUG AJ241823.1/282-335 .................AAUGAGACGAAACUCUUU AJ247122.1/132-52 UAUUGCUUUACUCCCG.CACAAGCCGAAACUGGA. AJ005300.1/282-335 .................AAUGAGACGAAACUCUUG AJ005302.1/281-334 .................AUUGAGACGAAACUCUUG AJ005318.1/56-3 .................GAUACGGUGAAACUUAUG AF339739.1/56-3 .................GAUACGGCGAAACUUAUG AJ241838.1/56-3 .................AAUGCGGCAAAACUUUUG AJ247121.1/133-53 UUUCGCUUUACUCCCG.CACAAGCCGAAACUGGA. AJ550911.1/282-335 .................AAUGAGACGAAACUCUUC AJ550898.1/282-335 .................AAUAAGACGAAACUCUUC AF170516.1/283-335 .................AAUGAGACGAAACUCUUC AJ005319.1/56-3 .................GAUACGGCGAAACUUAUG AJ550899.1/56-3 .................GAUAAGGCGAAACUUAUG AF170519.1/55-3 .................GAUACGGCGAAACUUAUG AJ247116.1/133-53 GAAAGCUUUACUCCCA.CACAAGCCGAAACUGGA. AJ550907.1/281-333 .................GAUGAGACGAAACUCUUC AJ241850.1/282-334 .................AAAGAGACGAAACUCUUU AF170499.1/56-3 .................AAUGCGGCGAAACUUUUG AF170520.1/282-335 .................AAUGAGACGAAACUUAUC AJ005299.1/282-335 .................AAUGAGACGAAACUCUUG AJ005312.1/282-335 .................AAUGAGACGAAACUCAUA AJ550909.1/282-333 ..................AUGAGACGAAACUCUUC AJ005322.1/281-334 .................AAUGAGACGAAACUCUUU AJ005294.1/282-334 .................AAUGAGACGAAACUCUUG AJ247123.1/132-52 GAAAGCUUUACUCCCG.CACAAGCCGAAACUGGA. AJ550900.1/56-3 .................GACAAGGCGAAACUUAUG AJ241830.1/282-334 .................AAUGAGACGAAACUCUUG AJ241831.1/281-334 .................AAUGAGACGAAACUCUUA M83545.1/282-335 .................GAUGAGACGAAACUCUUC AJ550910.1/282-336 .................GAUGAGACGAAACUCUUC AJ005314.1/281-334 .................AAUGAGACGAAACUCUUU Y12833.1/339-285 ...................AAGAACGAAAUAGUUA M63666.1/246-192 ...................AAGGACGAAACACCAG J02439.1/42-95 ...................AAGGACGAAACGGAUG J02386.1/42-95 ...................AAGGACGAAACGGAUG M33000.1/55-110 ..................AAAGGACGAAACAGCGC M33001.1/56-111 ..................AAAGGACGAAACAGCGC D00685.1/1-46 .....................GGACGAAACAGUA. M17439.1/1-48 ...................GAGGACGAAACAGGAC #=GC SS_cons .....................>>>>...>>>>>>. //pfam_tests.stk100644000765000024 3525213352276662 21753 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/t/data# STOCKHOLM 1.0 #=GF ID 14-3-3 #=GF AC PF00244.9 #=GF DE 14-3-3 protein #=GF AU Finn RD #=GF SE Prosite #=GF GA 25.00 25.00; 25.00 25.00; #=GF TC 28.50 28.50; 30.20 29.80; #=GF NC 22.70 22.70; 20.60 20.60; #=GF TP Domain #=GF BM hmmbuild -F HMM_ls SEED #=GF BM hmmcalibrate --seed 0 HMM_ls #=GF BM hmmbuild -f -F HMM_fs SEED #=GF BM hmmcalibrate --seed 0 HMM_fs #=GF AM globalfirst #=GF RN [1] #=GF RM 95327195 #=GF RT Structure of a 14-3-3 protein and implications for #=GF RT coordination of multiple signalling pathways. #=GF RA Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken #=GF RA A, Gamblin SJ; #=GF RL Nature 1995;376:188-191. #=GF RN [2] #=GF RM 95327196 #=GF RT Crystal structure of the zeta isoform of the 14-3-3 #=GF RT protein. #=GF RA Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington #=GF RA R; #=GF RL Nature 1995;376:191-194. #=GF RN [3] #=GF RM 96182649 #=GF RT Interaction of 14-3-3 with signaling proteins is mediated #=GF RT by the recognition of phosphoserine. #=GF RA Muslin AJ, Tanner JW, Allen PM, Shaw AS; #=GF RL Cell 1996;84:889-897. #=GF RN [4] #=GF RM 97424374 #=GF RT The 14-3-3 protein binds its target proteins with a common #=GF RT site located towards the C-terminus. #=GF RA Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T, #=GF RA Omata S, Ohno S, Isobe T #=GF RL FEBS Lett 1997;413:273-276. #=GF RN [5] #=GF RM 96394689 #=GF RT Molecular evolution of the 14-3-3 protein family. #=GF RA Wang W, Shakes DC #=GF RL J Mol Evol 1996;43:384-398. #=GF RN [6] #=GF RM 96300316 #=GF RT Function of 14-3-3 proteins. #=GF RA Jin DY, Lyu MS, Kozak CA, Jeang KT #=GF RL Nature 1996;382:308-308. #=GF RN [7] #=GF RM 12184815 #=GF RT The 14-3-3s. #=GF RA Ferl RJ, Manak MS, Reyes MF; #=GF RL Genome Biol 2002;3:REVIEWS3010. #=GF DR PROSITE; PDOC00633; #=GF DR SMART; 14_3_3; #=GF DR PRINTS; PR00305; #=GF DR SCOP; 1a4o; fa; #=GF DR INTERPRO; IPR000308; #=GF SQ 16 #=GS RAD25_SCHPO/5-240 AC P42657 #=GS RAD24_SCHPO/6-241 AC P42656 #=GS BMH1_YEAST/4-240 AC P29311 #=GS 1433E_SHEEP/4-239 AC P62262 #=GS 1433B_VICFA/7-242 AC P42654 #=GS 14334_LYCES/6-243 AC P42652 #=GS 14333_LYCES/9-246 AC P93209 #=GS 14336_ARATH/7-240 AC P48349 #=GS 14332_ENTHI/4-238 AC P42649 #=GS 14331_ENTHI/4-239 AC P42648 #=GS 1433T_HUMAN/3-236 AC P27348 #=GS 1433_XENLA/1-227 AC P29309 #=GS 1433Z_DROME/6-239 AC P29310 #=GS 14331_CAEEL/5-237 AC P41932 #=GS 1433F_RAT/3-240 AC P68511 #=GS 1433S_HUMAN/3-238 AC P31947 RAD25_SCHPO/5-240 RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHDVLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQVFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ RAD24_SCHPO/6-241 REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQDILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQAFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA BMH1_YEAST/4-240 REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDDILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG 1433E_SHEEP/4-239 REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG 1433B_VICFA/7-242 RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICIDVMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQAFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG 14334_LYCES/6-243 REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDGILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV 14333_LYCES/9-246 REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDGILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG 14336_ARATH/7-240 RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSGILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSD..... 14332_ENTHI/4-238 REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDDVLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADKSLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKEAFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE 14331_ENTHI/4-239 REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDDVLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQAFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE 1433T_HUMAN/3-236 KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE 1433_XENLA/1-227 .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE 1433Z_DROME/6-239 KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE 14331_CAEEL/5-237 VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQDVLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED 1433F_RAT/3-240 REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCNDVLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE 1433S_HUMAN/3-238 RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE #=GC seq_cons RE-hVYhAKLAEQAERY--MlpsMKpVsptss...ELSlEERNLLSVAYKNVlGARRASWRIISSIEQKEEu+G.N-c+lphIKEYRpKlEsELssICsDVLplLDcaLIPsA..ssuESKVFYhKMKGDYYRYLAEFsoG-cRKcss-sShtAYppApDIApuEhsPTHPIRLGLALNFSVFYYEILNSP-+ACpLAKQAFDEAIAELDTLsEESYKDSTLIMQLLRDNLTLWTSDhts-t // # STOCKHOLM 1.0 #=GF ID 2-ph_phosp #=GF AC PF04029.4 #=GF DE 2-phosphosulpholactate phosphatase #=GF AU Kerrison ND, Finn RD #=GF SE COG2045 #=GF GA 25.00 25.00; 25.00 25.00; #=GF TC 43.30 43.30; 28.00 28.00; #=GF NC 3.00 3.00; 22.60 22.00; #=GF TP Family #=GF BM hmmbuild -F HMM_ls SEED #=GF BM hmmcalibrate --seed 0 HMM_ls #=GF BM hmmbuild -f -F HMM_fs SEED #=GF BM hmmcalibrate --seed 0 HMM_fs #=GF AM globalfirst #=GF RN [1] #=GF RM 21474017 #=GF RT Identification of coenzyme M biosynthetic #=GF RT 2-phosphosulfolactate phosphatase. A member of a new class #=GF RT of Mg(2+)-dependent acid phosphatases. #=GF RA Graham DE, Graupner M, Xu H, White RH; #=GF RL Eur J Biochem 2001;268:5176-5188. #=GF DR INTERPRO; IPR005238; #=GF CC Thought to catalyse 2-phosphosulpholactate = sulpholactate + phosphate. #=GF CC Probable magnesium cofactor. Involved in the second step of coenzyme M #=GF CC biosynthesis. Inhibited by vanadate in Methanococcus jannaschii. Also #=GF CC known as the ComB family [1]. #=GF SQ 10 #=GS COMB_CLOAB/6-235 AC Q97E82 #=GS COMB_THEMA/1-224 AC Q9WZQ4 #=GS COMB_METTH/2-219 AC O27250 #=GS COMB_METJA/1-219 AC Q58540 #=GS COMB_DEIRA/2-232 AC Q9RUI6 #=GS COMB_SYNY3/2-241 AC P73849 #=GS COMB_THEVO/1-211 AC Q97CK6 #=GS COMB_THEAC/1-211 AC Q9HIA9 #=GS COMB_BACSU/2-223 AC O06738 #=GS COMB_STRCO/12-227 AC Q9F3E6 COMB_CLOAB/6-235 IISADDIKE.EKVKN..KTAVVIDMLRATSVITTALNNGCKRVVPVLTVEEALKKVKEY.GKDAILGGERKGLKIEGFDFSNSPMEY.TEDVV......KGKTLIMTTTNGTRAIKGSET.ARDILIGSVLNGEAVAEKIVELN.NDVVIVNAGTYGEFSIDDFICSGYIINCVMDRMKKLELT.DAATTA..QYVYKTNEDIKGFVKYAK.HYKRIMELGLKKDFEYCCKKDIVKLVPQYTN.GEIL.. COMB_THEMA/1-224 MVDVVMAPC.SPVEC..RTAVVIDVLRATSTIVTALSNGASGVIPVKTIEEALEKKK....EGVLICGERNAQKPKGFNLGNSPLEY.RKEKI......SGKTIVLTTTNGTQVIEKIRS..EEIIAASFLNLSAVVEYLKSKE..DILLVCAGTNGRFSLEDFLLAGAIV..KRLKRNDLG...DGAHAA..ERYFESVENTREEIKKHSSHAKRLISLGFENDIEFCTTEDLFKTVPALVN.GVFILK COMB_METTH/2-219 AMRIRLSFE.RPEGS..GLCIMVDLLRASATITAALDR.FREVIPVADIEEAMEYSR....KGYLVAGERGGETLPGF.IANSPLEV.KNYR........GDVLVLTTSNGTRILESVKS...DALVGCLNNLDAVAEAARELS.DEVEVVMAGVNGRFAIEDFLCAGEIIAAIDGEMDEYA...EASVLA..VQDRSLVDDAIRRSRSAER....LGGLGFMDDVEYCIKRNITGNVPVYRD.GRIELM COMB_METJA/1-219 MITLCNRFT..EYKC.GNVAIVVDVLRASTTITTLLSF.IDEVYITTST.....SKK....ENAIYIGERKGRKIEGFDFGNSPTEILANKDIIKERYENGEKVILTTTNGTRVLKSLDA..EHIFIGAIVNAKYVAKAVEDFE..DVSLVPCHRENNFAIDDFIGCGVIAKYLNGEFDEF.....IKAAL..ELTKHDWMSLILNSSSAEN....LKNLGYEKDVTFAILENSIDAVGIYKK...DKSK COMB_DEIRA/2-232 RLRVDLLPD..SHYP..DVALVIDVLRATTTAVTLLEQGAAELLLTRTTEAALAVRETV..PDVLLAGERGGLTIPGFDLGNSPVEV.SGGAV......AGRRVVMTTTNGTIAAHRAAQTARHVVLAALVNAHAVARHALAVASEEIAIVCAGTDGRVGLDDVYAAGVIA.EYLLALGDFQVD.DGARIA..LTMRRGGGDPGEALRSSG.HGATLARLGLSSDVDYAAQLSTSRLIPTLVP.GDDVPA COMB_SYNY3/2-241 EIFVYHTPELTPDQSLPDCAVVIDVLRATTTIATALKVGAEAVQVFSSLDDLMATSESWPGEKRLRAGERGGAAVAGYDLGNSPLDC.TSELM......AGKRLFLSTTNGTRALQRVKDC.PQLVTASLVNRGAAVDYLAQTQPKTVWLLGSGWEGGYSLEDTVCAGAIASLLREKGIDFTVGNDEVVAA..QSLYRQWRSDLLNLFKQASHGQRLLKLDRLEDLRYCATEDLIDILPKQVSPGVLTAA COMB_THEVO/1-211 MIRIADGRK.EENWS..SINIIIDIFRSTTTIPVILSRGARYIVPFKDVTSALNFKRKN..KNVVLIGEKYGIKPPFFDYDNSPAQI.INADL......EGKIIAFTSTNGMYVLSRIKR..GRILFSSLVNMSATIKKVKGKD..DILVVPSNRPIGKAVEDNIFAEMLK..LALEGKNY....DREILV..NRIRETKENTVVSISTQ..............DLEICLKLDLLDCVPEYIE.GKIVND COMB_THEAC/1-211 MIRIGDGRK.SDSWA..EINVVVDIFRSTTTIPMILFRGAKYILPFRDVRKAIEFKRRN..PGTILVGEKYGIKPPYFDYDNSPAEI.AEADL......SGKVVAFTSTNGTYVLSRIRS..GRIIFSSYVNLSATVAMIRSQR..DVLILPSNRPIGKAPEDILFANLLK..LMAEGHEV....DVSEYT..RKTEEINRNIIAGVGER..............DLEFCLRVDHTNIVPEYID.GRIVQS COMB_BACSU/2-223 PIAIYQGHH..HSLAPADINIVIDVIRAFTVAHYAFIGGAKEILLVRTADEAFALKDTY..PDYVLTGEEKGVGISGFDLDNSPKRM.AGQNM......TDKSLIQKTTNGVTAALGALN.AKHLFVTGFSNAKTTAQHVKKLVANDCVINIVASHP.SGDDDMACAEYIK..GIIEGTNV.....VTAAE..AIERIKGSSVAEKFFDCR......QPLFDSEDIVYCTKELTGDFVMKVKQDGEVPTI COMB_STRCO/12-227 DTRFVGIPE..VGEA.PAVAVVVDVMRAFTVAAWAFARGAEKIVLAGSLDEALALKERD..PARVAL..KDGPLTPGFDLVNSPGLL.RSADL......AGRTVVQKTTAGTVGALAVRD.ASLVLCAGFVVAEATARVLRARAPEHVTFVVTGEDG.RADEDLACARYIA..RRAAGHDA....DAAGFLGRAAESRAATELVQGVRQGVH..........PDDVALCLELDRFPFAMVAAP..EDSLM #=GC seq_cons hIclspshc.psstu..clAlVIDVLRATTTIssALspGAccllsspol--AlthK+p...cssllsGERtGhplsGFDluNSPhEl.sstcl......sGKsllhTTTNGTpslppl+s..pcllhuulVNtcAsActl+shs.pDVhlVsuGpsGthulEDhlsAGhIt..lttctc-h....Dsushs..pphccsscssltslppst.....lhtLsh.cDl-aChccDhhchVPphhs.Gcls.t // # STOCKHOLM 1.0 #=GF ID 3-alpha #=GF AC PF03475.3 #=GF DE 3-alpha domain #=GF AU Aravind L, Anantharaman V #=GF SE Aravind L, Anantharaman V #=GF GA 25.00 25.00; 25.00 25.00; #=GF TC 25.40 25.40; 25.00 25.00; #=GF NC 24.40 24.40; 24.60 24.60; #=GF TP Domain #=GF BM hmmbuild -F HMM_ls SEED #=GF BM hmmcalibrate --seed 0 HMM_ls #=GF BM hmmbuild -f -F HMM_fs SEED #=GF BM hmmcalibrate --seed 0 HMM_fs #=GF AM globalfirst #=GF RC See figure 2. #=GF RN [1] #=GF RM 11886751 #=GF RT MOSC domains: ancient, predicted sulfur-carrier domains, #=GF RT present in diverse metal--sulfur cluster biosynthesis #=GF RT proteins including Molybdenum cofactor sulfurases. #=GF RA Anantharaman V, Aravind L; #=GF RL FEMS Microbiol Lett 2002;207:55-61. #=GF DR SCOP; 1o67; fa; #=GF DR INTERPRO; IPR005163; #=GF DR PDB; 1o65 A; 178; 224; #=GF DR PDB; 1o65 B; 178; 224; #=GF DR PDB; 1o65 C; 178; 224; #=GF DR PDB; 1o67 A; 178; 224; #=GF DR PDB; 1o67 B; 178; 224; #=GF DR PDB; 1o67 C; 178; 224; #=GF CC This small triple helical domain has been predicted #=GF CC to assume a topology similar to helix-turn-helix #=GF CC domains. These domains are found at the C-terminus #=GF CC of proteins related to Swiss:P32157. #=GF SQ 11 #=GS Y278_HAEIN/174-219 AC P43976 #=GS Q99RT6_STAAM/171-217 AC Q99RT6 #=GS Q9PHR4_CAMJE/164-215 AC Q9PHR4 #=GS Q9RT82_DEIRA/181-226 AC Q9RT82 #=GS Q9KF70_BACHD/170-214 AC Q9KF70 #=GS Q9I1P0_PSEAE/174-219 AC Q9I1P0 #=GS Q9I607_PSEAE/169-215 AC Q9I607 #=GS O86804_STRCO/189-233 AC O86804 #=GS P95151_MYCTU/201-244 AC P95151 #=GS YIIM_ECOLI/168-214 AC P32157 #=GS O34542_BACSU/173-219 AC O34542 #=GS YIIM_ECOLI/168-214 DR PDB; 1o65 A; 178; 224; #=GS YIIM_ECOLI/168-214 DR PDB; 1o65 B; 178; 224; #=GS YIIM_ECOLI/168-214 DR PDB; 1o65 C; 178; 224; #=GS YIIM_ECOLI/168-214 DR PDB; 1o67 A; 178; 224; #=GS YIIM_ECOLI/168-214 DR PDB; 1o67 B; 178; 224; #=GS YIIM_ECOLI/168-214 DR PDB; 1o67 C; 178; 224; Y278_HAEIN/174-219 QITIRHLNRLLSTP.....KNEAELDSALEIEV.LAEAFKRSIRSQISKFKQ Q99RT6_STAAM/171-217 RLSVQQLNDLYYNDRQ....NQDMLRYALNNPF.LSPTRRDKLQKMYNRTLK Q9PHR4_CAMJE/164-215 SLSVFELNQLFYSPHQILKQNPNLLDKLEKLNSLISQNWHETIHKRLKNTYD Q9RT82_DEIRA/181-226 APTIGELFDADFAKSH....DPAELRAWLTFP..LGKRQRKEVEKWLAKAEG Q9KF70_BACHD/170-214 HPTVLEVNQLYYPKDI....NKEQLRRMSQLPE.LADAWKKAFSKKLANA.. Q9I1P0_PSEAE/174-219 DWSLLRLSEVLFDRRA....DAELLRQCLPLP..LTPSWRRTLERRLEKGQV Q9I607_PSEAE/169-215 ELTVARLLQWYFGDPL....EPLGLRQMMACDA.LSQRWRKTAAKRLSSGVV O86804_STRCO/189-233 EVTVALQFRAVTTQ.......RELLPRLLAAGGALHPEALATARKYVAEYGA P95151_MYCTU/201-244 NVTVGLVFRARTSE.......SELLPQLLAADA.LAAELKAYARERTPSPPP YIIM_ECOLI/168-214 DVTVQEAAAIAWHMPF....DDDQYHRLLSAAG.LSKSWTRTMQKRRLSGKI #=GR YIIM_ECOLI/168-214 SS SCBHHHHHHHHHTSCC....CHHHHHHHHTSTT.CCHHHHHHHHHHHHHSSC #=GR YIIM_ECOLI/168-214 SA 6000320010013274....3372052026033.108303630350385563 O34542_BACSU/173-219 GISVQFANRINYHDAK....NLTAIERILSEAA.LSESWRASFMKKKDRLLP #=GC SS_cons SCBHHHHHHHHHTSCC....CHHHHHHHHTSTT.CCHHHHHHHHHHHHHSSC #=GC SA_cons 6000320010013274....3372052026033.108303630350385563 #=GC seq_cons plTVtclsclhasc......stphLcphLshss.Lupsa+cohpK+lspshs //author-pod-syntax.t100644000765000024 45413352276662 21701 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/t#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } # This file was automatically generated by Dist::Zilla::Plugin::PodSyntaxTests. use strict; use warnings; use Test::More; use Test::Pod 1.41; all_pod_files_ok(); author-pod-coverage.t100644000765000024 53613352276662 22147 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/t#!perl BEGIN { unless ($ENV{AUTHOR_TESTING}) { print qq{1..0 # SKIP these tests are for testing by the author\n}; exit } } # This file was automatically generated by Dist::Zilla::Plugin::PodCoverageTests. use Test::Pod::Coverage 1.08; use Pod::Coverage::TrustPod; all_pod_coverage_ok({ coverage_class => 'Pod::Coverage::TrustPod' }); testaln.stockholm100644000765000024 4673113352276662 22466 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/t/data# STOCKHOLM 1.0 #=GF ID 14-3-3 #=GF AC PF00244 #=GF DE 14-3-3 proteins #=GF AU Finn RD #=GF AL Clustalw #=GF SE Prosite #=GF GA 25 25 #=GF TC 35.40 35.40 #=GF NC 8.80 8.80 #=GF BM hmmbuild -f HMM SEED #=GF BM hmmcalibrate --seed 0 HMM #=GF RN [1] #=GF RM 95327195 #=GF RT Structure of a 14-3-3 protein and implications for #=GF RT coordination of multiple signalling pathways. #=GF RA Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken #=GF RA A, Gamblin SJ; #=GF RL Nature 1995;376:188-191. #=GF RN [2] #=GF RM 95327196 #=GF RT Crystal structure of the zeta isoform of the 14-3-3 #=GF RT protein. #=GF RA Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington #=GF RA R; #=GF RL Nature 1995;376:191-194. #=GF RN [3] #=GF RM 96182649 #=GF RT Interaction of 14-3-3 with signaling proteins is mediated #=GF RT by the recognition of phosphoserine. #=GF RA Muslin AJ, Tanner JW, Allen PM, Shaw AS; #=GF RL Cell 1996;84:889-897. #=GF RN [4] #=GF RM 97424374 #=GF RT The 14-3-3 protein binds its target proteins with a common #=GF RT site located towards the C-terminus. #=GF RA Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T, #=GF RA Omata S, Ohno S, Isobe T #=GF RL FEBS Lett 1997;413:273-276. #=GF RN [5] #=GF RM 96394689 #=GF RT Molecular evolution of the 14-3-3 protein family. #=GF RA Wang W, Shakes DC #=GF RL J Mol Evol 1996;43:384-398. #=GF RN [6] #=GF RM 96300316 #=GF RT Function of 14-3-3 proteins. #=GF RA Jin DY, Lyu MS, Kozak CA, Jeang KT #=GF RL Nature 1996;382:308-308. #=GF DR PROSITE; PDOC00633; #=GF DR SMART; 14_3_3; #=GF DR PRINTS; PR00305; #=GF DR SCOP; 1a4o; fa; #=GF DR INTERPRO; IPR000308; #=GF SQ 16 #=GS 1433_LYCES/9-246 AC P93209 #=GS 1431_ENTHI/4-239 AC P42648 #=GS 1432_ENTHI/4-238 AC P42649 #=GS 1434_LYCES/6-243 AC P42652 #=GS 143B_VICFA/7-242 AC P42654 #=GS 1433_CAEEL/5-237 AC P41932 #=GS 143Z_DROME/6-239 AC P29310 #=GS 1433_XENLA/1-227 AC P29309 #=GS 143E_HUMAN/4-239 AC P42655 #=GS 143F_MOUSE/3-240 AC P11576 #=GS 143R_ARATH/7-245 AC P42647 #=GS 143S_HUMAN/3-238 AC P31947 #=GS 143T_HUMAN/3-236 AC P27348 #=GS BMH1_YEAST/4-240 AC P29311 #=GS RA24_SCHPO/6-241 AC P42656 #=GS RA25_SCHPO/5-240 AC P42657 1433_LYCES/9-246 REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDGILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG 1434_LYCES/6-243 REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDGILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV 143R_ARATH/7-245 RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSGILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDYAGAD 143B_VICFA/7-242 RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICIDVMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQAFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG 143E_HUMAN/4-239 REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG BMH1_YEAST/4-240 REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDDILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG RA24_SCHPO/6-241 REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQDILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQAFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA RA25_SCHPO/5-240 RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHDVLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQVFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ 1431_ENTHI/4-239 REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDDVLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQAFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE 1432_ENTHI/4-238 REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDDVLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADKSLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKEAFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE 1433_CAEEL/5-237 VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQDVLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED 143Z_DROME/6-239 KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE 1433_XENLA/1-227 .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE 143T_HUMAN/3-236 KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE 143F_MOUSE/3-240 REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCNDVLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE 143S_HUMAN/3-238 RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE // # STOCKHOLM 1.0 #=GF ID 14-3-3 #=GF AC PF00245 #=GF DE 14-3-3 proteins #=GF AU Finn RD #=GF AL Clustalw #=GF SE Prosite #=GF GA 25 25 #=GF TC 35.40 35.40 #=GF NC 8.80 8.80 #=GF BM hmmbuild -f HMM SEED #=GF BM hmmcalibrate --seed 0 HMM #=GF RN [1] #=GF RM 95327195 #=GF RT Structure of a 14-3-3 protein and implications for #=GF RT coordination of multiple signalling pathways. #=GF RA Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken #=GF RA A, Gamblin SJ; #=GF RL Nature 1995;376:188-191. #=GF RN [2] #=GF RM 95327196 #=GF RT Crystal structure of the zeta isoform of the 14-3-3 #=GF RT protein. #=GF RA Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington #=GF RA R; #=GF RL Nature 1995;376:191-194. #=GF RN [3] #=GF RM 96182649 #=GF RT Interaction of 14-3-3 with signaling proteins is mediated #=GF RT by the recognition of phosphoserine. #=GF RA Muslin AJ, Tanner JW, Allen PM, Shaw AS; #=GF RL Cell 1996;84:889-897. #=GF RN [4] #=GF RM 97424374 #=GF RT The 14-3-3 protein binds its target proteins with a common #=GF RT site located towards the C-terminus. #=GF RA Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T, #=GF RA Omata S, Ohno S, Isobe T #=GF RL FEBS Lett 1997;413:273-276. #=GF RN [5] #=GF RM 96394689 #=GF RT Molecular evolution of the 14-3-3 protein family. #=GF RA Wang W, Shakes DC #=GF RL J Mol Evol 1996;43:384-398. #=GF RN [6] #=GF RM 96300316 #=GF RT Function of 14-3-3 proteins. #=GF RA Jin DY, Lyu MS, Kozak CA, Jeang KT #=GF RL Nature 1996;382:308-308. #=GF DR PROSITE; PDOC00633; #=GF DR SMART; 14_3_3; #=GF DR PRINTS; PR00305; #=GF DR SCOP; 1a4o; fa; #=GF DR INTERPRO; IPR000308; #=GF SQ 16 #=GS 1433_LYCES/9-246 AC P93209 #=GS 1431_ENTHI/4-239 AC P42648 #=GS 1432_ENTHI/4-238 AC P42649 #=GS 1434_LYCES/6-243 AC P42652 #=GS 143B_VICFA/7-242 AC P42654 #=GS 1433_CAEEL/5-237 AC P41932 #=GS 143Z_DROME/6-239 AC P29310 #=GS 1433_XENLA/1-227 AC P29309 #=GS 143E_HUMAN/4-239 AC P42655 #=GS 143F_MOUSE/3-240 AC P11576 #=GS 143R_ARATH/7-245 AC P42647 #=GS 143S_HUMAN/3-238 AC P31947 #=GS 143T_HUMAN/3-236 AC P27348 #=GS BMH1_YEAST/4-240 AC P29311 #=GS RA24_SCHPO/6-241 AC P42656 #=GS RA25_SCHPO/5-240 AC P42657 1433_LYCES/9-246 REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDGILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG 1434_LYCES/6-243 REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDGILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV 143R_ARATH/7-245 RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSGILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDYAGAD 143B_VICFA/7-242 RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICIDVMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQAFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG 143E_HUMAN/4-239 REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG BMH1_YEAST/4-240 REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDDILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG RA24_SCHPO/6-241 REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQDILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQAFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA RA25_SCHPO/5-240 RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHDVLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQVFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ 1431_ENTHI/4-239 REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDDVLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQAFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE 1432_ENTHI/4-238 REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDDVLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADKSLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKEAFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE 1433_CAEEL/5-237 VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQDVLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED 143Z_DROME/6-239 KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE 1433_XENLA/1-227 .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE 143T_HUMAN/3-236 KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE 143F_MOUSE/3-240 REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCNDVLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE 143S_HUMAN/3-238 RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE // # STOCKHOLM 1.0 #=GF ID 14-3-3 #=GF AC PF00246 #=GF DE 14-3-3 proteins #=GF AU Finn RD #=GF AL Clustalw #=GF SE Prosite #=GF GA 25 25 #=GF TC 35.40 35.40 #=GF NC 8.80 8.80 #=GF BM hmmbuild -f HMM SEED #=GF BM hmmcalibrate --seed 0 HMM #=GF RN [1] #=GF RM 95327195 #=GF RT Structure of a 14-3-3 protein and implications for #=GF RT coordination of multiple signalling pathways. #=GF RA Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken #=GF RA A, Gamblin SJ; #=GF RL Nature 1995;376:188-191. #=GF RN [2] #=GF RM 95327196 #=GF RT Crystal structure of the zeta isoform of the 14-3-3 #=GF RT protein. #=GF RA Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington #=GF RA R; #=GF RL Nature 1995;376:191-194. #=GF RN [3] #=GF RM 96182649 #=GF RT Interaction of 14-3-3 with signaling proteins is mediated #=GF RT by the recognition of phosphoserine. #=GF RA Muslin AJ, Tanner JW, Allen PM, Shaw AS; #=GF RL Cell 1996;84:889-897. #=GF RN [4] #=GF RM 97424374 #=GF RT The 14-3-3 protein binds its target proteins with a common #=GF RT site located towards the C-terminus. #=GF RA Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T, #=GF RA Omata S, Ohno S, Isobe T #=GF RL FEBS Lett 1997;413:273-276. #=GF RN [5] #=GF RM 96394689 #=GF RT Molecular evolution of the 14-3-3 protein family. #=GF RA Wang W, Shakes DC #=GF RL J Mol Evol 1996;43:384-398. #=GF RN [6] #=GF RM 96300316 #=GF RT Function of 14-3-3 proteins. #=GF RA Jin DY, Lyu MS, Kozak CA, Jeang KT #=GF RL Nature 1996;382:308-308. #=GF DR PROSITE; PDOC00633; #=GF DR SMART; 14_3_3; #=GF DR PRINTS; PR00305; #=GF DR SCOP; 1a4o; fa; #=GF DR INTERPRO; IPR000308; #=GF SQ 16 #=GS 1433_LYCES/9-246 AC P93209 #=GS 1431_ENTHI/4-239 AC P42648 #=GS 1432_ENTHI/4-238 AC P42649 #=GS 1434_LYCES/6-243 AC P42652 #=GS 143B_VICFA/7-242 AC P42654 #=GS 1433_CAEEL/5-237 AC P41932 #=GS 143Z_DROME/6-239 AC P29310 #=GS 1433_XENLA/1-227 AC P29309 #=GS 143E_HUMAN/4-239 AC P42655 #=GS 143F_MOUSE/3-240 AC P11576 #=GS 143R_ARATH/7-245 AC P42647 #=GS 143S_HUMAN/3-238 AC P31947 #=GS 143T_HUMAN/3-236 AC P27348 #=GS BMH1_YEAST/4-240 AC P29311 #=GS RA24_SCHPO/6-241 AC P42656 #=GS RA25_SCHPO/5-240 AC P42657 1433_LYCES/9-246 REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDGILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG 1434_LYCES/6-243 REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDGILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV 143R_ARATH/7-245 RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSGILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDYAGAD 143B_VICFA/7-242 RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICIDVMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQAFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG 143E_HUMAN/4-239 REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG BMH1_YEAST/4-240 REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDDILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG RA24_SCHPO/6-241 REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQDILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQAFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA RA25_SCHPO/5-240 RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHDVLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQVFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ 1431_ENTHI/4-239 REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDDVLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQAFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE 1432_ENTHI/4-238 REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDDVLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADKSLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKEAFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE 1433_CAEEL/5-237 VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQDVLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED 143Z_DROME/6-239 KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE 1433_XENLA/1-227 .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE 143T_HUMAN/3-236 KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE 143F_MOUSE/3-240 REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCNDVLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE 143S_HUMAN/3-238 RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE // Index000755000765000024 013352276662 20046 5ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/lib/BioStockholm.pm100644000765000024 3124613352276662 22535 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/lib/Bio/Index# # BioPerl module for Bio::Index::Stockholm # # Please direct questions and support issues to # # Cared for by Chris Fields # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Index::Stockholm - Interface for indexing Stockholm files =head1 SYNOPSIS use strict; use Bio::Index::Stockholm; my ($indexfile,$file1,$file2,$query); my $index = Bio::Index::Stockholm->new(-filename => $indexfile, -write_flag => 1); $index->make_index($file1,$file2); # get raw data stream starting at alignment position my $fh = $index->get_stream($query); # fetch individual alignment my $align = $index->fetch_aln($query); # alias for fetch_report my $align = $index->fetch_report($query); # same as above print "query is ", $align->display_id, "\n"; =head1 DESCRIPTION Indexes Stockholm format alignments such as those from Pfam and Rfam. Returns raw stream data using the ID or a Bio::SimpleAlign object (via Bio::AlignIO). This module also allows for ID parsing using a callback: $inx->id_parser(\&get_id); # make the index $inx->make_index($file_name); # here is where the retrieval key is specified sub get_id { my $line = shift; $line =~ /^>.+gi\|(\d+)/; $1; } The indexer is capable of indexing based on multiple IDs passed back from the callback; this is assuming of course all IDs are unique. The default is to use the alignment ID provided for Rfam/Pfam output. Note: for best results 'use strict'. =head1 TODO - allow using an alternative regex for indexing (for instance, the ID instead of AC) =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHOR - Chris Fields Email cjfields-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Index::Stockholm; $Bio::Index::Stockholm::VERSION = '1.7.3'; use strict; use Bio::AlignIO; use base qw(Bio::Index::Abstract Bio::Root::Root); sub _version { return ${Bio::Root::Version::VERSION}; } =head2 new Usage : $index = Bio::Index::Abstract->new( -filename => $dbm_file, -write_flag => 0, -dbm_package => 'DB_File', -verbose => 0); Function: Returns a new index object. If filename is specified, then open_dbm() is immediately called. Bio::Index::Abstract->new() will usually be called directly only when opening an existing index. Returns : A new index object Args : -filename The name of the dbm index file. -write_flag TRUE if write access to the dbm file is needed. -dbm_package The Perl dbm module to use for the index. -verbose Print debugging output to STDERR if TRUE. =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); } =head2 Bio::Index::Stockholm implemented methods =cut =head2 fetch_report Title : fetch_report Usage : my $align = $idx->fetch_report($id); Function: Returns a Bio::SimpleAlign object for a specific alignment Returns : Bio::SimpleAlign Args : valid id =cut sub fetch_report{ my ($self,$id) = @_; my $fh = $self->get_stream($id); my $report = Bio::AlignIO->new(-noclose => 1, -format => 'stockholm', -fh => $fh); return $report->next_aln; } =head2 fetch_aln Title : fetch_aln Usage : my $align = $idx->fetch_aln($id); Function: Returns a Bio::SimpleAlign object for a specific alignment Returns : Bio::SimpleAlign Args : valid id Note : alias for fetch_report =cut *fetch_aln = \&fetch_report; =head2 Require methods from Bio::Index::Abstract =cut =head2 _index_file Title : _index_file Usage : $index->_index_file( $file_name, $i ) Function: Specialist function to index report file(s). Is provided with a filename and an integer by make_index in its SUPER class. Example : Returns : Args : =cut sub _index_file { my( $self, $file, # File name $i # Index-number of file being indexed ) = @_; my $begin = 0; my $id_parser = $self->id_parser; open my $STOCKHOLM, '<', $file or $self->throw("Could not read file '$file': $!"); my %done_ids; # In Windows, text files have '\r\n' as line separator, but when reading in # text mode Perl will only show the '\n'. This means that for a line "ABC\r\n", # "length $_" will report 4 although the line is 5 bytes in length. # We assume that all lines have the same line separator and only read current line. my $init_pos = tell($STOCKHOLM); my $curr_line = <$STOCKHOLM>; my $pos_diff = tell($STOCKHOLM) - $init_pos; my $correction = $pos_diff - length $curr_line; seek $STOCKHOLM, $init_pos, 0; # Rewind position to proceed to read the file while (<$STOCKHOLM>) { if ( /^#\sSTOCKHOLM/ ) { $begin = tell($STOCKHOLM) - length($_) - $correction; } for my $id ( &$id_parser($_) ) { next if exists $done_ids{$id}; $self->add_record($id, $i, $begin) if $id; $done_ids{$id} = 1; } %done_ids = () if ( m{//} ); } close $STOCKHOLM; 1; } =head2 id_parser Title : id_parser Usage : $index->id_parser( CODE ) Function: Stores or returns the code used by record_id to parse the ID for record from a string. Returns \&default_id_parser (see below) if not set. An entry will be added to the index for each string in the list returned. Example : $index->id_parser( \&my_id_parser ) Returns : reference to CODE if called without arguments Args : CODE =cut sub id_parser { my ($self,$code) = @_; if ($code) { $self->{'_id_parser'} = $code; } return $self->{'_id_parser'} || \&default_id_parser; } =head2 default_id_parser Title : default_id_parser Usage : $id = default_id_parser($line) Function: The default parser for Stockholm.pm Returns : Array of specified ids Args : a line string =cut sub default_id_parser { my $line = shift; my %accs; if ( $line =~ /^#=GF AC\s+(\S+)/ ) { $accs{$1}++; } keys %accs; } =head2 Bio::Index::Abstract methods =cut =head2 filename Title : filename Usage : $value = $self->filename(); $self->filename($value); Function: Gets or sets the name of the dbm index file. Returns : The current value of filename Args : Value of filename if setting, or none if getting the value. =head2 write_flag Title : write_flag Usage : $value = $self->write_flag(); $self->write_flag($value); Function: Gets or sets the value of write_flag, which is whether the dbm file should be opened with write access. Returns : The current value of write_flag (default 0) Args : Value of write_flag if setting, or none if getting the value. =head2 dbm_package Usage : $value = $self->dbm_package(); $self->dbm_package($value); Function: Gets or sets the name of the Perl dbm module used. If the value is unset, then it returns the value of the package variable $USE_DBM_TYPE or if that is unset, then it chooses the best available dbm type, choosing 'DB_File' in preference to 'SDBM_File'. Bio::Abstract::Index may work with other dbm file types. Returns : The current value of dbm_package Args : Value of dbm_package if setting, or none if getting the value. =head2 get_stream Title : get_stream Usage : $stream = $index->get_stream( $id ); Function: Returns a file handle with the file pointer at the approprite place This provides for a way to get the actual file contents and not an object WARNING: you must parse the record deliminter *yourself*. Abstract won't do this for you So this code $fh = $index->get_stream($myid); while( <$fh> ) { # do something } will parse the entire file if you do not put in a last statement in, like while( <$fh> ) { /^\/\// && last; # end of record # do something } Returns : A filehandle object Args : string represents the accession number Notes : This method should not be used without forethought =head2 open_dbm Usage : $index->open_dbm() Function: Opens the dbm file associated with the index object. Write access is only given if explicitly asked for by calling new(-write => 1) or having set the write_flag(1) on the index object. The type of dbm file opened is that returned by dbm_package(). The name of the file to be is opened is obtained by calling the filename() method. Example : $index->_open_dbm() Returns : 1 on success =head2 _version Title : _version Usage : $type = $index->_version() Function: Returns a string which identifes the version of an index module. Used to permanently identify an index file as having been created by a particular version of the index module. Must be provided by the sub class Example : Returns : Args : none =head2 _filename Title : _filename Usage : $index->_filename( FILE INT ) Function: Indexes the file Example : Returns : Args : =head2 _file_handle Title : _file_handle Usage : $fh = $index->_file_handle( INT ) Function: Returns an open filehandle for the file index INT. On opening a new filehandle it caches it in the @{$index->_filehandle} array. If the requested filehandle is already open, it simply returns it from the array. Example : $fist_file_indexed = $index->_file_handle( 0 ); Returns : ref to a filehandle Args : INT =head2 _file_count Title : _file_count Usage : $index->_file_count( INT ) Function: Used by the index building sub in a sub class to track the number of files indexed. Sets or gets the number of files indexed when called with or without an argument. Example : Returns : INT Args : INT =head2 add_record Title : add_record Usage : $index->add_record( $id, @stuff ); Function: Calls pack_record on @stuff, and adds the result of pack_record to the index database under key $id. If $id is a reference to an array, then a new entry is added under a key corresponding to each element of the array. Example : $index->add_record( $id, $fileNumber, $begin, $end ) Returns : TRUE on success or FALSE on failure Args : ID LIST =head2 pack_record Title : pack_record Usage : $packed_string = $index->pack_record( LIST ) Function: Packs an array of scalars into a single string joined by ASCII 034 (which is unlikely to be used in any of the strings), and returns it. Example : $packed_string = $index->pack_record( $fileNumber, $begin, $end ) Returns : STRING or undef Args : LIST =head2 unpack_record Title : unpack_record Usage : $index->unpack_record( STRING ) Function: Splits the sting provided into an array, splitting on ASCII 034. Example : ( $fileNumber, $begin, $end ) = $index->unpack_record( $self->db->{$id} ) Returns : A 3 element ARRAY Args : STRING containing ASCII 034 =head2 DESTROY Title : DESTROY Usage : Called automatically when index goes out of scope Function: Closes connection to database and handles to sequence files Returns : NEVER Args : NONE =cut 1; AlignIO000755000765000024 013352276662 20261 5ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/lib/Biostockholm.pm100644000765000024 6431213352276662 23010 0ustar00cjfieldsstaff000000000000Bio-AlignIO-stockholm-1.7.3/lib/Bio/AlignIO# # BioPerl module for Bio::AlignIO::stockholm # # Based on the Bio::SeqIO::stockholm module # by Ewan Birney # and Lincoln Stein # # and the SimpleAlign.pm module of Ewan Birney # # Copyright Peter Schattner, Chris Fields # # You may distribute this module under the same terms as perl itself # _history # September 5, 2000 # November 6, 2006 - completely refactor read_aln(), add write_aln() # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::stockholm - stockholm sequence input/output stream =head1 SYNOPSIS # Do not use this module directly. Use it via the L class. use Bio::AlignIO; use strict; my $in = Bio::AlignIO->new(-format => 'stockholm', -file => 't/data/testaln.stockholm'); while( my $aln = $in->next_aln ) { } =head1 DESCRIPTION This object can transform L objects to and from stockholm flat file databases. This has been completely refactored from the original stockholm parser to handle annotation data and now includes a write_aln() method for (almost) complete stockholm format output. Stockholm alignment records normally contain additional sequence-based and alignment-based annotation GF Lines (alignment feature/annotation): #=GF Placed above the alignment GC Lines (Alignment consensus) #=GC Placed below the alignment GS Lines (Sequence annotations) #=GS GR Lines (Sequence meta data) #=GR Currently, sequence annotations (those designated with GS tags) are parsed only for accession numbers and descriptions. It is intended that full parsing will be added at some point in the near future along with a builder option for optionally parsing alignment annotation and meta data. The following methods/tags are currently used for storing and writing the alignment annotation data. Tag SimpleAlign Method ---------------------------------------------------------------------- AC accession ID id DE description ---------------------------------------------------------------------- Tag Bio::Annotation TagName Parameters Class ---------------------------------------------------------------------- AU SimpleValue record_authors value SE SimpleValue seed_source value GA SimpleValue gathering_threshold value NC SimpleValue noise_cutoff value TC SimpleValue trusted_cutoff value TP SimpleValue entry_type value SQ SimpleValue num_sequences value PI SimpleValue previous_ids value DC Comment database_comment comment CC Comment alignment_comment comment DR Target dblink database primary_id comment AM SimpleValue build_method value NE SimpleValue pfam_family_accession value NL SimpleValue sequence_start_stop value SS SimpleValue sec_structure_source value BM SimpleValue build_model value RN Reference reference * RC Reference reference comment RM Reference reference pubmed RT Reference reference title RA Reference reference authors RL Reference reference location ---------------------------------------------------------------------- * RN is generated based on the number of Bio::Annotation::Reference objects =head2 Custom annotation Some users may want to add custom annotation beyond those mapped above. Currently there are two methods to do so; however, the methods used for adding such annotation may change in the future, particularly if alignment Writer classes are introduced. In particular, do not rely on changing the global variables @WRITEORDER or %WRITEMAP as these may be made private at some point. 1) Use (and abuse) the 'custom' tag. The tagname for the object can differ from the tagname used to store the object in the AnnotationCollection. # AnnotationCollection from the SimpleAlign object my $coll = $aln->annotation; my $factory = Bio::Annotation::AnnotationFactory->new(-type => Bio::Annotation::SimpleValue'); my $rfann = $factory->create_object(-value => $str, -tagname => 'mytag'); $coll->add_Annotation('custom', $rfann); $rfann = $factory->create_object(-value => 'foo', -tagname => 'bar'); $coll->add_Annotation('custom', $rfann); OUTPUT: # STOCKHOLM 1.0 #=GF ID myID12345 #=GF mytag katnayygqelggvnhdyddlakfyfgaglealdffnnkeaaakiinwvaEDTTRGKIQDLV?? #=GF mytag TPtd~????LDPETQALLV???????????????????????NAIYFKGRWE?????????~?? #=GF mytag ??HEF?A?EMDTKPY??DFQH?TNen?????GRI??????V???KVAM??MF?????????N?? #=GF mytag ???DD?VFGYAEL????DE???????L??D??????A??TALELAY?????????????????? #=GF mytag ?????????????KG??????Sa???TSMLILLP???????????????D?????????????? #=GF mytag ???????????EGTr?????AGLGKLLQ??QL????????SREef??DLNK??L???AH????R #=GF mytag ????????????L????????????????????????????????????????R?????????R #=GF mytag ??QQ???????V???????AVRLPKFSFefefdlkeplknlgmhqafdpnsdvfklmdqavlvi #=GF mytag gdlqhayafkvd???????????????????????????????????????????????????? #=GF mytag ???????????????????????????????????????????????????????????????? #=GF mytag ???????????????????????????????????????????????????????????????? #=GF mytag ???????????????????????????????????????????????????????????????? #=GF mytag ?????????????INVDEAG?TEAAAATAAKFVPLSLppkt??????????????????PIEFV #=GF mytag ADRPFAFAIR??????E?PAT?G????SILFIGHVEDPTP?msv? #=GF bar foo ... 2) Modify the global @WRITEORDER and %WRITEMAP. # AnnotationCollection from the SimpleAlign object my $coll = $aln->annotation; # add to WRITEORDER my @order = @Bio::AlignIO::stockholm::WRITEORDER; push @order, 'my_stuff'; @Bio::AlignIO::stockholm::WRITEORDER = @order; # make sure new tag maps to something $Bio::AlignIO::stockholm::WRITEMAP{my_stuff} = 'Hobbit/SimpleValue'; my $rfann = $factory->create_object(-value => 'Frodo', -tagname => 'Hobbit'); $coll->add_Annotation('my_stuff', $rfann); $rfann = $factory->create_object(-value => 'Bilbo', -tagname => 'Hobbit'); $coll->add_Annotation('my_stuff', $rfann); OUTPUT: # STOCKHOLM 1.0 #=GF ID myID12345 #=GF Hobbit Frodo #=GF Hobbit Bilbo .... =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues =head1 AUTHORS - Chris Fields, Peter Schattner Email: cjfields-at-uiuc-dot-edu, schattner@alum.mit.edu =head1 CONTRIBUTORS Andreas Kahari, ak-at-ebi.ac.uk Jason Stajich, jason-at-bioperl.org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::AlignIO::stockholm; $Bio::AlignIO::stockholm::VERSION = '1.7.3'; use strict; use Bio::Seq::Meta; use Bio::AlignIO::Handler::GenericAlignHandler; use Text::Wrap qw(wrap); use base qw(Bio::AlignIO); my $STKVERSION = 'STOCKHOLM 1.0'; # This maps the two-letter annotation key to a Annotation/parameter/tagname # combination. Some data is stored using get/set methods ('Methods') The rest # is mapped to Annotation objects using the parameter for the parsed data # and the tagname for, well, the Annotation tagname. A few are treated differently # based on the type of data stored (Reference data in particular). my %MAPPING = ( 'AC' => 'ACCESSION', 'ID' => 'ID', 'DE' => ['DESCRIPTION' => 'DESCRIPTION'], 'AU' => ['RECORD_AUTHORS' => 'RECORD_AUTHORS'], 'SE' => 'SEED_SOURCE', 'BM' => 'BUILD_COMMAND', 'GA' => 'GATHERING_THRESHOLD', 'NC' => 'NOISE_CUTOFF', 'TC' => 'TRUSTED_CUTOFF', 'TP' => 'ENTRY_TYPE', 'SQ' => 'NUM_SEQUENCES', 'PI' => 'PREVIOUS_IDS', 'DC' => ['DATABASE_COMMENT' => 'DATABASE_COMMENT'], 'DR' => 'DBLINK', 'RN' => ['REFERENCE' => 'REFERENCE'], 'RC' => ['REFERENCE' => 'COMMENT'], 'RM' => ['REFERENCE' => 'PUBMED'], 'RT' => ['REFERENCE' => 'TITLE'], 'RA' => ['REFERENCE' => 'AUTHORS'], 'RL' => ['REFERENCE' => 'JOURNAL'], 'CC' => ['ALIGNMENT_COMMENT' => 'ALIGNMENT_COMMENT'], #Pfam-specific 'AM' => 'BUILD_METHOD', 'NE' => 'PFAM_FAMILY_ACCESSION', 'NL' => 'SEQ_START_STOP', # Rfam-specific GF lines #'SS' => 'SEC_STRUCTURE_SOURCE', 'SEQUENCE' => 'SEQUENCE' ); # this is the order that annotations are written our @WRITEORDER = qw(accession id description previous_ids record_authors seed_source sec_structure_source gathering_threshold trusted_cutoff noise_cutoff entry_type build_command build_method pfam_family_accession seq_start_stop reference database_comment custom dblink alignment_comment num_sequences seq_annotation ); # This maps the tagname back to a tagname-annotation value combination. # Some data is stored using get/set methods ('Methods'), others # are mapped b/c of more complex annotation types. our %WRITEMAP = ( 'accession' => 'AC/Method', 'id' => 'ID/Method', 'description' => 'DE/Method', 'record_authors' => 'AU/SimpleValue', 'seed_source' => 'SE/SimpleValue', 'build_command' => 'BM/SimpleValue', 'gathering_threshold' => 'GA/SimpleValue', 'noise_cutoff' => 'NC/SimpleValue', 'trusted_cutoff' => 'TC/SimpleValue', 'entry_type' => 'TP/SimpleValue', 'num_sequences' => 'SQ/SimpleValue', 'previous_ids' => 'PI/SimpleValue', 'database_comment' => 'DC/SimpleValue', 'dblink' => 'DR/DBLink', 'reference' => 'RX/Reference', 'ref_number' => 'RN/number', 'ref_comment' => 'RC/comment', 'ref_pubmed' => 'RM/pubmed', 'ref_title' => 'RT/title', 'ref_authors' => 'RA/authors', 'ref_location' => 'RL/location', 'alignment_comment' => 'CC/Comment', 'seq_annotation' => 'DR/Collection', #Pfam-specific 'build_method' => 'AM/SimpleValue', 'pfam_family_accession' => 'NE/SimpleValue', 'seq_start_stop' => 'NL/SimpleValue', # Rfam-specific GF lines 'sec_structure_source' => 'SS/SimpleValue', # custom; this is used to carry over anything from the input alignment # not mapped to LocatableSeqs or SimpleAlign in a meaningful way 'custom' => 'XX/SimpleValue' ); # This maps the tagname back to a tagname-annotation value combination. # Some data is stored using get/set methods ('Methods'), others # are mapped b/c of more complex annotation types. =head2 new Title : new Usage : my $alignio = Bio::AlignIO->new(-format => 'stockholm' -file => '>file'); Function: Initialize a new L reader or writer Returns : L object Args : -line_length : length of the line for the alignment block -alphabet : symbol alphabet to set the sequences to. If not set, the parser will try to guess based on the alignment accession (if present), defaulting to 'dna'. -spaces : (optional, def = 1) boolean to add a space in between the "# STOCKHOLM 1.0" header and the annotation and the annotation and the alignment. =cut sub _initialize { my ( $self, @args ) = @_; $self->SUPER::_initialize(@args); my ($handler, $linelength, $spaces) = $self->_rearrange([qw(HANDLER LINE_LENGTH SPACES)],@args); $spaces = defined $spaces ? $spaces : 1; $self->spaces($spaces); # hash for functions for decoding keys. $handler ? $self->alignhandler($handler) : $self->alignhandler(Bio::AlignIO::Handler::GenericAlignHandler->new( -format => 'stockholm', -verbose => $self->verbose, )); $linelength && $self->line_length($linelength); } =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Returns : L object Args : NONE =cut sub next_aln { my $self = shift; my $handler = $self->alignhandler; # advance to alignment header while( defined(my $line = $self->_readline) ) { if ($line =~ m{^\#\s*STOCKHOLM\s+}xmso) { last; } } $self->{block_line} = 0; # go into main body of alignment my ($data_chunk, $isa_primary, $name, $alphabet); my $last_feat = ''; while( defined(my $line = $self->_readline) ) { # only blank lines are in between blocks, so reset block line my ($primary_tag, $secondary_tag, $data, $nse, $feat, $align, $concat); if ($line =~ m{^\s*$}xmso) { $self->{block_line} &&= 0; next; } # End of Record if (index($line, '//') == 0) { # fencepost $handler->data_handler($data_chunk); undef $data_chunk; $handler->data_handler({ALIGNMENT => 1, NAME => 'ALPHABET', DATA => $self->alphabet}) if $self->alphabet; last; } elsif ($line =~ m{^\#=([A-Z]{2})\s+([^\n]+?)\s*$}xmso) { ($primary_tag, $data) = ($1, $2); if ($primary_tag eq 'GS' || $primary_tag eq 'GR') { ($nse, $feat, $data) = split(/\s+/, $data, 3); } else { ($feat, $data) = split(/\s+/, $data, 2); } $align = ($primary_tag eq 'GF' || $primary_tag eq 'GR') ? 1 : 0; } elsif ($line =~ m{^(\S+)\s+([^\s]+)\s*}) { $self->{block_line}++; ($feat, $nse, $data) = ('SEQUENCE', $1, $2); } else { $self->debug("Missed line : $line\n"); } $primary_tag ||= ''; # when no #= line is present $align ||= 0; # array refs where the two values are equal indicate the start of a # primary chunk of data, otherwise it is to be folded into the last # data chunk under a secondary tag. These are also concatenated # to previous values if the if (exists($MAPPING{$feat}) && ref $MAPPING{$feat} eq 'ARRAY') { ($name, $secondary_tag, $isa_primary) = ( $MAPPING{$feat}->[0] eq $MAPPING{$feat}->[1] ) ? ($MAPPING{$feat}->[0], 'DATA', 1) : (@{ $MAPPING{$feat} }, 0) ; $concat = $last_feat eq $feat ? 1 : 0; } elsif (exists($MAPPING{$feat})) { ($name, $secondary_tag, $isa_primary) = ($MAPPING{$feat}, 'DATA', 1); # catch alphabet here if possible if ($align && $name eq 'ACCESSION' && !$self->alphabet) { if ($data =~ m{^(P|R)F}) { $self->alphabet($1 eq 'R' ? 'rna' : $1 eq 'P' ? 'protein' : undef ); } } } else { $name = ($primary_tag eq 'GR') ? 'NAMED_META' : ($primary_tag eq 'GC') ? 'CONSENSUS_META' : 'CUSTOM'; ($secondary_tag, $isa_primary) = ('DATA', 1); } # Since we can't determine whether data should be passed into the # Handler until the next round (due to concatenation and combining # data), we always check for the presence of the last chunk when the # occasion calls for it (i.e. when the current data string needs to go # into a new data chunk). If the data needs to be concatenated it is # flagged above and checked below (and passed by if the conditions # warrant it). # We run into a bit of a fencepost problem, (one chunk left over at # the end); that is taken care of above when the end of the record is # found. if ($isa_primary && defined $data_chunk && !$concat) { $handler->data_handler($data_chunk); undef $data_chunk; } $data_chunk->{NAME} = $name; # used for the handler $data_chunk->{ALIGNMENT} = $align; # flag that determines chunk destination $data_chunk->{$secondary_tag} .= (defined($data_chunk->{$secondary_tag})) ? ' '.$data : $data; $data_chunk->{NSE} = $nse if $nse; if ($name eq 'SEQUENCE' || $name eq 'NAMED_META' || $name eq 'CONSENSUS_META') { $data_chunk->{BLOCK_LINE} = $self->{block_line}; $data_chunk->{META_TAG} = $feat if ($name ne 'SEQUENCE'); } $last_feat = $feat; } my $aln = $handler->build_alignment; $handler->reset_parameters; return $aln; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in stockholm format Returns : 1 for success and 0 for error Args : L object =cut { my %LINK_CB = ( 'PDB' => sub {join('; ',($_[0]->database, $_[0]->primary_id.' '. ($_[0]->optional_id || ''), $_[0]->start, $_[0]->end)).';'}, 'SCOP' => sub {join('; ',($_[0]->database, $_[0]->primary_id || '', $_[0]->optional_id)).';'}, '_DEFAULT_' => sub {join('; ',($_[0]->database, $_[0]->primary_id)).';'}, ); sub write_aln { # enable array of SimpleAlign objects as well (see clustalw write_aln()) my ($self, @aln) = @_; for my $aln (@aln) { $self->throw('Need Bio::Align::AlignI object') if (!$aln || !($aln->isa('Bio::Align::AlignI'))); my $coll = $aln->annotation; my ($aln_ann, $seq_ann) = ('#=GF ', '#=GS '); $self->_print("# $STKVERSION\n") || return 0; $self->spaces && $self->_print("\n"); # annotations first #=GF XX .... for my $param (@WRITEORDER) { my @anns; # no point in going through this if there is no annotation! last if !$coll; # alignment annotations my $ct = 1; $self->throw("Bad parameter: $param") if !exists $WRITEMAP{$param}; # get the data, act on it based on the tag my ($tag, $key) = split q(/), $WRITEMAP{$param}; if ($key eq 'Method') { push @anns, $aln->$param; } else { @anns = $coll->get_Annotations($param); } my $rn = 1; ANNOTATIONS: for my $ann (@anns) { # using Text::Wrap::wrap() for word wrap my ($text, $alntag, $data); if ($tag eq 'RX') { REFS: for my $rkey (qw(ref_comment ref_number ref_pubmed ref_title ref_authors ref_location)) { my ($newtag, $method) = split q(/), $WRITEMAP{$rkey}; $alntag = sprintf('%-10s',$aln_ann.$newtag); if ($rkey eq 'ref_number') { $data = "[$rn]"; } else { $data = $ann->$method; } next REFS unless $data; $text = wrap($alntag, $alntag, $data); $self->_print("$text\n") or return 0; } $rn++; next ANNOTATIONS; } elsif ($tag eq 'XX') { # custom my $newtag = $ann->tagname; my $tmp = $aln_ann.$newtag; $alntag = sprintf('%-*s',length($tmp) + 1, $tmp); $data = $ann->display_text; } elsif ($tag eq 'SQ') { # use the actual number, not the stored Annotation data my $tmp = $aln_ann.$tag; $alntag = sprintf('%-*s',length($tmp) + 1, $tmp); $data = $aln->num_sequences; } elsif ($tag eq 'DR') { my $tmp = $aln_ann.$tag; $alntag = sprintf('%-*s',length($tmp) + 1, $tmp); my $db = uc $ann->database; my $cb = exists $LINK_CB{$db} ? $LINK_CB{$db} : $LINK_CB{_DEFAULT_}; $data = $ann->display_text($cb); } else { my $tmp = $aln_ann.$tag; $alntag = sprintf('%-*s',length($tmp) + 1, $tmp); $data = ref $ann ? $ann->display_text : $ann; } next unless $data; $text = wrap($alntag, $alntag, $data); $self->_print("$text\n") || return 0; } } #=GS AC xxxxxx my $tag = 'AC'; for my $seq ($aln->each_seq) { if (my $acc = $seq->accession_number) { my $text = sprintf("%-4s%-22s %-3s%s\n",$seq_ann, $aln->displayname($seq->get_nse), $tag, $acc); $self->_print($text) || return 0; } } #=GS DR xxxxxx $tag = 'DR'; for my $sf ($aln->get_SeqFeatures) { if (my @links = $sf->annotation->get_Annotations('dblink')) { for my $link (@links) { my $db = uc $link->database; my $cb = exists $LINK_CB{$db} ? $LINK_CB{$db} : $LINK_CB{_DEFAULT_}; my $text = sprintf("%-4s%-22s%-3s%s\n",$seq_ann, $aln->displayname($sf->entire_seq->get_nse), $tag, $link->display_text($cb)); $self->_print($text) || return 0; } } } $self->spaces && $self->_print("\n"); # now the sequences... my $blocklen = $self->line_length; my $maxlen = $aln->maxdisplayname_length() + 3; my $metalen = $aln->max_metaname_length() || 0; if ($blocklen) { my $blockstart = 1; my $alnlen = $aln->length; while ($blockstart < $alnlen) { my $subaln = $aln->slice($blockstart, $blockstart+$blocklen-1 ,1); $self->_print_seqs($subaln,$maxlen,$metalen); $blockstart += $blocklen; $self->_print("\n") unless $blockstart >= $alnlen; } } else { $self->_print_seqs($aln,$maxlen,$metalen); } $self->_print("//\n") || return 0; } $self->flush() if $self->_flush_on_write && defined $self->_fh; return 1; } } =head2 line_length Title : line_length Usage : $obj->line_length($newval) Function: Set the alignment output line length Returns : value of line_length Args : newvalue (optional) =cut sub line_length { my ( $self, $value ) = @_; if ( defined $value ) { $self->{'_line_length'} = $value; } return $self->{'_line_length'}; } =head2 spaces Title : spaces Usage : $obj->spaces(1) Function: Set the 'spaces' flag, which prints extra newlines between the header and the annotation and the annotation and the alignment Returns : sequence data type Args : newvalue (optional) =cut sub spaces { my $self = shift; return $self->{'_spaces'} = shift if @_; return $self->{'_spaces'}; }; =head2 alignhandler Title : alignhandler Usage : $stream->alignhandler($handler) Function: Get/Set the Bio::HandlerBaseI object Returns : Bio::HandlerBaseI Args : Bio::HandlerBaseI =cut sub alignhandler { my ($self, $handler) = @_; if ($handler) { $self->throw("Not a Bio::HandlerBaseI") unless ref($handler) && $handler->isa("Bio::HandlerBaseI"); $self->{'_alignhandler'} = $handler; } return $self->{'_alignhandler'}; } ############# PRIVATE INIT/HANDLER METHODS ############# sub _print_seqs { my ($self, $aln, $maxlen, $metalen) = @_; my ($seq_meta, $aln_meta) = ('#=GR','#=GC'); # modified (significantly) from AlignIO::pfam my ($namestr,$seq,$add); # pad extra for meta lines for $seq ( $aln->each_seq() ) { my ($s, $e, $str) = ($seq->start, $seq->end, $seq->strand); $namestr = $aln->displayname($seq->get_nse()); $self->_print(sprintf("%-*s%s\n",$maxlen+$metalen, $namestr, $seq->seq())) || return 0; if ($seq->isa('Bio::Seq::MetaI')) { for my $mname ($seq->meta_names) { $self->_print(sprintf("%-*s%s\n",$maxlen+$metalen, $seq_meta.' '.$namestr.' '.$mname, $seq->named_meta($mname))) || return 0; } } } # alignment consensus my $ameta = $aln->consensus_meta; if ($ameta) { for my $mname ($ameta->meta_names) { $self->_print(sprintf("%-*s%s\n",$maxlen+$metalen, $aln_meta.' '.$mname, $ameta->named_meta($mname))) || return 0; } } } 1;