<!DOCTYPE html>
<html lang="en">
<head>
<title>SequenceServer: Custom BLAST Server</title>
<meta name="author" content="Anurag Priyam" />
<meta name="author" content="Ben J. Woodcroft" />
<meta name="author" content="Yannick Wurm" />
<meta name="author" content="Cedric Wurm" />
<meta name="description" content="Custom BLAST server provided by SequenceServer (http://www.sequenceserver.com)"/>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
<script type="text/javascript" src="<%= uri('/js/jquery.js') %>"></script>
<script type="text/javascript" src="<%= uri('/js/jquery.enablePlaceholder.min.js') %>"></script>
<script type="text/javascript" src="<%= uri('/js/jquery.activity.js') %>"></script>
<script type="text/javascript" src="<%= uri('/js/sequenceserver.js') %>"></script>
<script type="text/javascript" src="<%= uri('/js/sequenceserver.blast.js') %>"></script>
<%# without a space after erb's closing tag, a / gets appended to css' path %>
<link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/bootstrap.min.css') %>" />
<link rel="stylesheet" media="screen" type="text/css" href="<%= uri('/css/custom.css') %>" />
</head>
<body>
<div class="container">
<div class="page">
<div class="page-header" id="banner">
<h1>BLAST Sequence(s)</h1>
</div>
<form method="post" action="<%= uri('/#result') %>">
<div class="row">
<div class="span12">
<div class="offset-left sequence">
<div class="clearfix">
<textarea name="sequence" id="sequence" rows="11" spellcheck="false" <%= 'autofocus="true"' unless @blast %> placeholder="Paste your sequence(s) here..." ></textarea>
</div>
</div>
</div>
<div class="span4">
<div class="offset-right box blastmethods">
<div class="clearfix">
<fieldset>
<legend><h4>Blast methods</h4></legend>
<ul class="inputs-list">
<li>
<label title="Protein query; protein database.">
<input type="radio" name="method" value="blastp" id="blastp"/>
<span>blastp</span>
</label>
</li>
<li>
<label title="Protein query; six frame translated nucleotide database.">
<input type="radio" name="method" value="tblastn" id="tblastn"/>
<span>tblastn</span>
</label>
</li>
<li>
<label title="Nucleotide query; nucleotide database.">
<input type="radio" name="method" value="blastn" id="blastn"/>
<span>blastn</span>
</label>
</li>
<li>
<label title="Translated nucleotide query; protein database">
<input type="radio" name="method" value="blastx" id="blastx"/>
<span>blastx</span>
</label>
</li>
<li>
<label title="Six-frame translated nucleotide query; six-frame translated nucleotide database">
<input type="radio" name="method" value="tblastx" id="tblastx"/>
<span>tblastx</span>
</label>
</li>
</ul>
</fieldset>
</div>
</div>
</div>
</div>
<div class="row">
<div class="span8">
<div class="offset-left box databases nucleotide">
<div class="clearfix">
<fieldset>
<legend><h4>Nucleotide databases</h4></legend>
<ul class="inputs-list">
<% settings.databases['nucleotide'].each_with_index do |db, i| %>
<li>
<label>
<input type="checkbox" id="ndb<%=i%>" name="db[nucleotide][]" value="<%=i%>"/>
<span> <%= db.title or db.name %></span>
</label>
</li>
<% end %>
</ul>
</fieldset>
</div>
</div>
</div>
<div class="span8">
<div class="offset-right box databases protein">
<div class="clearfix">
<fieldset>
<legend><h4>Protein databases</h4></legend>
<ul class="inputs-list">
<% settings.databases['protein'].each_with_index do |db, i| %>
<li>
<label>
<input type="checkbox" id="pdb<%=i%>" name="db[protein][]" value="<%=i%>"/>
<span> <%= db.title or db.name %></span>
</label>
</li>
<% end %>
</ul>
</fieldset>
</div>
</div>
</div>
</div>
<div class="row">
<div class="span12">
<div class="offset-left box advanced">
<div class="clearfix">
<label class="span4" for="advanced"><h4 title="Click to show/hide advanced options.">Advanced Parameters:</h4></label>
<input class="span8" type="text" name="advanced" id="advanced" title="View, and enter advanced parameters." placeholder="eg: -evalue 1.0e-5 -num_alignments 100"/>
</div>
<pre class="help">
<%= ERB::Util.h %q|
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = `10'
-word_size <Integer, >=2>
Word size for wordfinder algorithm
-gapopen <Integer>
Cost to open a gap
-gapextend <Integer>
Cost to extend a gap
-matrix <String>
Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats <String>
Use composition-based statistics for blastp / tblastn:
D or d: default (equivalent to 2)
0 or F or f: no composition-based statistics
1: Composition-based statistics as in NAR 29:2994-3005, 2001
2 or T or t : Composition-based score adjustment as in Bioinformatics
21:902-911,
2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911,
2005, unconditionally
For programs other than tblastn, must either be absent or be D, F or 0
Default = `2'
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Default = `500'
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
*** Query filtering options
-seg <String>
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
'no' to disable)
Default = `no'
-soft_masking <Boolean>
Apply filtering locations as soft masks
Default = `false'
-lcase_masking
Use lower case filtering in query and subject sequence(s)?
*** Restrict search or results
-gilist <String>
Restrict search of database to list of GI's
* Incompatible with: negative_gilist, seqidlist, remote, subject,
subject_loc
-seqidlist <String>
Restrict search of database to list of SeqId's
* Incompatible with: gilist, negative_gilist, remote, subject,
subject_loc
-negative_gilist <String>
Restrict search of database to everything except the listed GIs
* Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String>
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask <String>
Filtering algorithm ID to apply to the BLAST database as soft masking
* Incompatible with: subject, subject_loc
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
* Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)>
Best Hit algorithm overhang value (recommended value: 0.1)
* Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)>
Best Hit algorithm score edge value (recommended value: 0.1)
* Incompatible with: culling_limit
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep | %>
</pre>
</div>
</div>
<div class="span4">
<input type="submit" class="btn large primary" value="BLAST!"/>
</div>
</div>
</form>
<div id="result" class="offset-left offset-right">
<%= @blast %>
</div>
<div id="underbar">
<p>© <a href='http://www.sequenceserver.com'>SequenceServer: BLAST search made easy!</a></p>
</div>
</div> <!-- /page -->
</div> <!-- /container -->
</body>
</html>