sequenceserver 0.8.5 → 0.8.6
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- data/lib/sequenceserver.rb +1 -1
- data/public/js/jquery.activity.js +1 -1
- data/sequenceserver.gemspec +1 -1
- metadata +31 -59
- data/lib/blast.rb~ +0 -200
- data/lib/sequenceserver/database_formatter.rb~ +0 -190
- data/public/css/beige.css~ +0 -226
- data/public/js/sequenceserver.js~ +0 -250
- data/tests/chromedriver.log +0 -98
- data/tests/database/nucleotide/head.fa +0 -10
- data/tests/database/nucleotide/head.faVno_parse.html +0 -96
- data/tests/database/nucleotide/head.faVparse.html +0 -96
- data/tests/database/nucleotide/headVno_parse.archive +0 -151
- data/tests/database/nucleotide/headVno_parse.archive.csv +0 -1
- data/tests/database/nucleotide/headVparse.archive +0 -148
- data/tests/database/nucleotide/headVparse.archive.csv +0 -1
- data/tests/database/nucleotide/no_parse.fa +0 -5486
- data/tests/database/nucleotide/no_parse.fa.nhr +0 -0
- data/tests/database/nucleotide/no_parse.fa.nin +0 -0
- data/tests/database/nucleotide/no_parse.fa.nsq +0 -0
- data/tests/database/nucleotide/no_parse.info +0 -7
- data/tests/database/nucleotide/parse.fa +0 -5486
- data/tests/database/nucleotide/parse.fa.nhr +0 -0
- data/tests/database/nucleotide/parse.fa.nin +0 -0
- data/tests/database/nucleotide/parse.fa.nog +0 -0
- data/tests/database/nucleotide/parse.fa.nsd +0 -946
- data/tests/database/nucleotide/parse.fa.nsi +0 -0
- data/tests/database/nucleotide/parse.fa.nsq +0 -0
- data/tests/database/nucleotide/parse.info +0 -7
- data/views/search.erb~ +0 -164
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xml:lang="en" lang="en" xmlns="http://www.w3.org/1999/xhtml">
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<head>
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<title>SequenceServer</title>
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<meta name="author" content="Anurag Priyam" />
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<meta name="author" content="Yannick Wurm" />
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<meta name="author" content="Cedric Wurm" />
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<meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
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<script type="text/javascript" src="/js/jquery.js"></script>
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<script type="text/javascript" src="/js/jquery.enablePlaceholder.min.js"></script>
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<script type="text/javascript" src="/js/search.js"></script>
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<link rel="stylesheet" media="screen" type="text/css" href="css/beige.css"/>
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</head>
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<body>
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<div class="container">
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<h1 class="banner">BLAST Sequence(s)</h1>
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<form method="post" action="/#result">
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<div class="horizontal">
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<div class="entryfield">
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<textarea name="sequence" id="sequence" rows="11" cols="" placeholder="Paste your sequence(s) here..." ></textarea>
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</div>
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<fieldset class="blastmethods box" >
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<div>
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<input type="radio" name="method" value="blastp" id="blastp" class="radiobutton" title="Protein query; protein database."/>
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<label for="blastp" title="Protein query; protein database.">blastp</label>
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</div>
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<div class="clear">
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<input type="radio" name="method" value="tblastn" id="tblastn" class="radiobutton" title="Protein query; six-frame translated nucleotide database." />
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<label for="tblastn" title="Protein query; six-frame translated nucleotide database.">tblastn</label>
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</div>
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<div class="clear">
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<input type="radio" name="method" value="blastn" id="blastn" class="radiobutton" title="Nucleotide query; nucleotide database."/>
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<label for="blastn" title="Nucleotide query; nucleotide database.">blastn</label>
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</div>
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<div class="clear">
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<input type="radio" name="method" value="blastx" id="blastx" class="radiobutton" title="Translated nucleotide query; protein database."/>
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<label for="blastx" title="Six-frame translated nucleotide query; protein database.">blastx</label>
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</div>
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<div class="clear">
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<input type="radio" name="method" value="tblastx" id="tblastx" class="radiobutton" title="Six-frame translated nucleotide query; six-frame translated nucleotide database"/>
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<label for="tblastx" title="Six-frame translated nucleotide query; six-frame translated nucleotide database">tblastx</label>
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</div>
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</fieldset>
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</div>
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<div class='horizontal'>
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<fieldset class="nucleotide rounded box databases">
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<h2>Nucleotide databases</h2>
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<!-- Database list is actually dynamically loaded -->
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<% settings.databases['nucleotide'].each_with_index do |db, i| %>
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<input type="checkbox" class="dbcheckbox" id="ndb<%=i%>" name="db[nucleotide][]" value="<%=i%>"/>
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<label for="ndb<%=i%>" class="dbdescription"><%= db.title or db.name %></label>
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<% end %>
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</fieldset>
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<fieldset class="protein rounded box databases">
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<h2>Protein databases</h2>
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<!-- Database list is actually dynamically loaded-->
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<% settings.databases['protein'].each_with_index do |db, i| %>
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<input type="checkbox" class="dbcheckbox" id="pdb<%=i%>" name="db[protein][]" value="<%=i%>"/>
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<label for="pdb<%=i%>" class="dbdescription"><%= db.title or db.name %></label>
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<% end %>
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</fieldset>
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</div>
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<div class="horizontal">
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<fieldset class="advanced box rounded">
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<span class="bigtext pointer" title="Click to show/hide advanced options.">Advanced parameters:</span>
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<input type="text" name="advanced" id="advanced" title="View, and enter advanced parameters." placeholder="eg: -evalue 1.0e-5 -num_alignments 100"/>
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<pre class="smalltext">
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<%= ERB::Util.h %q|
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-evalue <Real>
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Expectation value (E) threshold for saving hits
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Default = `10'
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-word_size <Integer, >=2>
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Word size for wordfinder algorithm
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-gapopen <Integer>
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Cost to open a gap
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-gapextend <Integer>
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Cost to extend a gap
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-matrix <String>
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Scoring matrix name (normally BLOSUM62)
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-threshold <Real, >=0>
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Minimum word score such that the word is added to the BLAST lookup table
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-comp_based_stats <String>
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Use composition-based statistics for blastp / tblastn:
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D or d: default (equivalent to 2)
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0 or F or f: no composition-based statistics
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1: Composition-based statistics as in NAR 29:2994-3005, 2001
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2 or T or t : Composition-based score adjustment as in Bioinformatics
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21:902-911,
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2005, conditioned on sequence properties
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3: Composition-based score adjustment as in Bioinformatics 21:902-911,
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2005, unconditionally
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For programs other than tblastn, must either be absent or be D, F or 0
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Default = `2'
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-num_descriptions <Integer, >=0>
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Number of database sequences to show one-line descriptions for
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Default = `500'
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-num_alignments <Integer, >=0>
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Number of database sequences to show alignments for
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Default = `250'
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*** Query filtering options
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-seg <String>
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Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
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'no' to disable)
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Default = `no'
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-soft_masking <Boolean>
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Apply filtering locations as soft masks
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Default = `false'
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-lcase_masking
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Use lower case filtering in query and subject sequence(s)?
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*** Restrict search or results
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-gilist <String>
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Restrict search of database to list of GI's
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* Incompatible with: negative_gilist, seqidlist, remote, subject,
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subject_loc
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-seqidlist <String>
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Restrict search of database to list of SeqId's
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* Incompatible with: gilist, negative_gilist, remote, subject,
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subject_loc
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-negative_gilist <String>
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Restrict search of database to everything except the listed GIs
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* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
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-entrez_query <String>
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Restrict search with the given Entrez query
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* Requires: remote
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-db_soft_mask <String>
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Filtering algorithm ID to apply to the BLAST database as soft masking
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* Incompatible with: subject, subject_loc
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-culling_limit <Integer, >=0>
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If the query range of a hit is enveloped by that of at least this many
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higher-scoring hits, delete the hit
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* Incompatible with: best_hit_overhang, best_hit_score_edge
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-best_hit_overhang <Real, (>0 and <0.5)>
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Best Hit algorithm overhang value (recommended value: 0.1)
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* Incompatible with: culling_limit
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-best_hit_score_edge <Real, (>0 and <0.5)>
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Best Hit algorithm score edge value (recommended value: 0.1)
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* Incompatible with: culling_limit
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-max_target_seqs <Integer, >=1>
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Maximum number of aligned sequences to keep | %>
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</pre>
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</fieldset>
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<div class="submit_button">
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<input type="submit" value="BLAST!"/>
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</div>
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</div>
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</form>
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<div class="result prepend-top" id="result">
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<pre class='smalltext'>
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<%= @blast %>
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</pre>
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</div>
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<div class ="underbar">
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<p>© <a href='http://www.sequenceserver.com'>sequenceserver.com</a></p>
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