ncbi_blast_results_parser 0.1.0

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source :rubygems
+
+gemspec

data/LICENCE

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+Copyright (c) 2013 Gareth Rees & Angharad Williams
+  
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# NCBI Blast Results Parser
+
+Parses useful information from the HTML response of an NCBI Blast.
+
+## Current Methods
+
+- `rid`: Parses a Request ID
+- `wait`: Parses the suggested wait time before attempting to get results
+- `status`: Parses the status of a Blast
+
+## Usage
+
+```ruby
+rid = NCBIBlastResultsParser.rid(response)
+#=> 'ABCD1234'
+
+wait = NCBIBlastResultsParser.wait(response)
+#=> 17
+
+status = NCBIBlastResultsParser.status(response)
+#=> 'READY'
+```
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.test_files = FileList['spec/lib/**/*_spec.rb']
+  t.verbose = true
+end
+
+task :default => :test

data/lib/ncbi_blast_results_parser.rb

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+require 'nokogiri'
+
+Dir[File.dirname(__FILE__) + '/ncbi_blast_results_parser/*.rb'].each do |file|
+  require file
+end
+
+module NCBIBlastResultsParser
+
+  # Parse a Request ID from an NCBI Blast
+  #
+  # Returns a String
+  def self.rid(response)
+    rid_parser = NCBIBlastResultsParser::RIDParser.new
+    parser     = Nokogiri::HTML::SAX::Parser.new(rid_parser)
+    parser.parse(response)
+    rid_parser.rid
+  end
+
+  # Parse the suggested wait time for an NCBI Blast
+  #
+  # Returns an Integer
+  def self.wait(response)
+    rid_parser = NCBIBlastResultsParser::RIDParser.new
+    parser     = Nokogiri::HTML::SAX::Parser.new(rid_parser)
+    parser.parse(response)
+    rid_parser.wait
+  end
+
+  # Parse the status from an NCBI Blast
+  #
+  # Returns a String
+  def self.status(response)
+    status_parser = NCBIBlastResultsParser::StatusParser.new
+    parser        = Nokogiri::HTML::SAX::Parser.new(status_parser)
+    parser.parse(response)
+    status_parser.status
+  end
+
+end

data/lib/ncbi_blast_results_parser/rid_parser.rb

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+module NCBIBlastResultsParser
+  class RIDParser < Nokogiri::XML::SAX::Document
+
+    attr_reader :rid, :wait
+
+    def comment(string)
+      parse_rid(string) if string.strip.include? 'RID ='
+      parse_wait_time(string) if string.strip.include? 'RTOE ='
+    end
+
+    def parse_rid(string)
+      line = string[/((?:RID =.*?$){1})/]
+      @rid = line.split.last
+    end
+
+    def parse_wait_time(string)
+      line  = string[/((?:RTOE =.*?$){1})/]
+      @wait = line.split.last.to_i
+    end
+
+  end
+end

data/lib/ncbi_blast_results_parser/status_parser.rb

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+module NCBIBlastResultsParser
+  class StatusParser < Nokogiri::XML::SAX::Document
+
+    attr_reader :status
+
+    def comment(string)
+      parse_status(string) if string.strip.include? 'Status='
+    end
+
+    def parse_status(string)
+      line    = string[/((?:Status=.*?$){1})/]
+      @status = line.split('=').last
+    end
+  end
+end

data/lib/ncbi_blast_results_parser/version.rb

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+module NCBIBlastResultsParser
+  VERSION = '0.1.0'
+end

data/ncbi_blast_results_parser.gemspec

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+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'ncbi_blast_results_parser/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = 'ncbi_blast_results_parser'
+  gem.version       = NCBIBlastResultsParser::VERSION
+  gem.authors       = ['Gareth Rees']
+  gem.email         = ['gareth@garethrees.co.uk']
+  gem.description   = %q{Parses useful information from the HTML response of an NCBI Blast}
+  gem.summary       = %q{Parses useful information from the HTML response of an NCBI Blast}
+  gem.homepage      = ''
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ['lib']
+
+  gem.add_dependency 'nokogiri'
+
+  gem.add_development_dependency 'minitest'
+  gem.add_development_dependency 'turn'
+  gem.add_development_dependency 'rake'
+end

data/spec/fixtures/ready_response.html

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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<meta name="jig" content="ncbitoggler"/>
+<meta name="ncbitoggler" content="animation:'none'"/>
+<title>NCBI Blast:</title>
+<script type="text/javascript" src="http://www.ncbi.nlm.nih.gov/core/jig/1.11/js/jig.min.js"></script>
+<link rel="stylesheet" type="text/css" href="css/main.css" media="screen" />
+<link rel="stylesheet" type="text/css" href="css/blastRes.css" media="screen" />
+<link rel="stylesheet" type="text/css" href="css/print.css" media="print" />
+<!--[if lte IE 6]>
+<link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
+<![endif]-->
+<script type="text/javascript" src="js/utils.js"></script>
+<script type="text/javascript" src="js/results.js"></script>
+</head>
+
+<body id="type-a" class="noToggleCheck" >
+<div id="wrap">
+			<div id="header">	    
+		<div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov" title="NCBI Home Page"><img src="css/images/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page" /></a>BLAST <span id="trdm"> &reg;</span><h1 class="desc">Basic Local Alignment Search Tool</h1>
+		</div>
+		<div id="search">
+		
+<div>
+<script language="JavaScript" type="text/javascript"><!--
+// --></script><table class="medium1" style="border:2px solid #336699;" cellpadding="2" cellspacing="0" id="myncbi_off"><tr><td
+bgcolor="#336699" align="left"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td
+bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img border="0"
+src="http://www.ncbi.nlm.nih.gov/corehtml/query/MyNCBI/myncbihelpicon.gif" alt="My NCBI help" /></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a
+href="http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015" title="Click to sign in"
+onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015');return false;">[Sign In]</a> <a
+href="http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015" title="Click to register for an account"
+onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/account/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FALIGNMENTS%3D200%26ALIGNMENT%5FTYPE%3DPairwise%26CMD%3DGet%26DESCRIPTIONS%3D100%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3DXML%26OLD%5FBLAST%3Dfalse%26OVERVIEW%3Dyes%26RID%3DHZMF5DEN015');return false;">[Register]</a></td></tr></table></div>
+		</div>
+		<a class="skp" href="#content-wrap">Jump to Page Content</a>		
+		<ul id="nav">
+                <li  class="first "><a href="Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
+                <li  class="recent "><a href="Blast.cgi?CMD=GetSaved&amp;RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li>                
+                <li  class="saved "><a href="Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST search parameters">Saved Strategies</a></li>
+                <li  class= "last documentation "> <a href="Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs" title="BLAST documentation">Help</a></li>                
+                </ul>
+    </div>
+
+        <div id="content-wrap">
+
+                <div id="breadcrumb" class="inlineDiv">
+                   <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/
+                   <a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST</a>/
+                   <a href="Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=">blastn suite</a>/
+                   <strong>Formatting Results - HZMF5DEN015</strong>             
+                </div>
+                <div class="inlineDiv resHeader">				   
+				   <a  id="frmPage"  class="WAITING" href="#" submitForm="reformat">[Formatting options] </a>                   
+                </div>
+                <h3 id="jtitle" >Job Title: </h3>
+								
+                <div id="content">                
+                <!--<ul id="msg" class="msg"><li class=""><p class=""></p><p class=""></p><p class=""></p></ul> -->
+                <ul id="msg" class="msg"><li class=""></li></ul>
+                <p><!--
+                QBlastInfoBegin
+	                Status=READY
+                QBlastInfoEnd
+                --></p> 
+                               
+                <SCRIPT LANGUAGE="JavaScript"><!--
+                    var tm = "2000";
+                    if (tm != "") {                    
+                        setTimeout('document.forms[0].submit();',tm);
+                    }
+                //--></SCRIPT>                                
+                <table id="statInfo" class="WAITING">
+                <tr><td>Request ID</td><td> <b>HZMF5DEN015</b></td></tr>
+                <tr class="odd"><td>Status</td><td>Searching</td></tr>
+                <tr><td>Submitted at</td><td>Sat Feb 16 13:37:25 2013</td></tr>
+                <tr class="odd"><td>Current time</td><td>Sat Feb 16 13:37:26 2013</td></tr>
+                <tr><td>Time since submission</td><td>00:00:01</td></tr>
+                </table>
+                <p class="WAITING">This page will be automatically updated in <b>2</b> seconds</p>       
+                <form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" id="results">
+                <input name="ALIGNMENTS" type="hidden" value="200"><input name="ALIGNMENT_TYPE" type="hidden" value="Pairwise"><input name="DESCRIPTIONS" type="hidden" value="100"><input name="FORMAT_OBJECT" type="hidden" value="Alignment"><input name="FORMAT_TYPE" type="hidden" value="XML"><input name="OLD_BLAST" type="hidden" value="false"><input name="OVERVIEW" type="hidden" value="yes"><input name="RID" type="hidden" value="HZMF5DEN015"><input name="SEARCH_DB_STATUS" type="hidden" value="31"><input name="USER_TYPE" type="hidden" value="2"><input name="_PGR" type="hidden" value="0">                
+                <input name="_PGR" type="hidden" value="0" >
+                <input name="CMD" type="hidden" value="Get">
+               
+                </form>
+                                
+				</div><!-- /#content -->
+				<form action="Blast.cgi" enctype="application/x-www-form-urlencoded"  method="post" name="reformat" id="reformat">				
+				   <input name="QUERY_INFO" type="hidden" value="" />    				
+				   <input name="ENTREZ_QUERY" type="hidden" value="" />
+                   <input name="CDD_RID" type="hidden" value="" />
+                   <input name="CDD_SEARCH_STATE" type="hidden" value="" />
+                   <input name="RID" type="hidden" value="HZMF5DEN015" />
+				   <input name="STEP_NUMBER" type="hidden" value="" />
+				   <input name="CMD" type="hidden" value="Web"/>				
+				   <input NAME="PAGE_TYPE" type="hidden"  value="BlastFormatting"/>
+				
+				   <!-- TO DO: test all of those changes -->				   	
+				   <!-- Psi blast params  PSI_BLAST_PARAMS - commented- using forms[0] from fromatter> -->
+				   <!-- Current Formatting options FORMATTING_OPTIONS- commented- using forms[0] from fromatter> -->
+				   <!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> -->
+                 </form>				
+        </div><!-- /#content-wrap -->
+
+		    	
+<div id="footer">
+   <div id="rgs">BLAST is a registered trademark of the National Library of Medicine.</div> 
+   <p id="orgns">
+      <a href="http://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information">NCBI</a> |
+      <a href="http://www.nlm.nih.gov/" title="National Library of Medicine">NLM</a> |
+      <a href="http://www.nih.gov/" title="National Institutes of Health">NIH</a> |
+      <a href="http://www.hhs.gov/" title="US Department of Health and Human Services">DHHS</a>
+   </p>
+   
+   <p>
+      <a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html'
+      title='NCBI intellectual property statement'>Copyright</a> | 
+      <a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html#disclaimer'
+      title='About liability, endorsements, external links, pop-up advertisements'>Disclaimer</a> | 
+      <a href='http://www.nlm.nih.gov/privacy.html'
+      title='NLM privacy policy'>Privacy</a> | 
+      <a href='http://www.ncbi.nlm.nih.gov/About/accessibility.html'
+      title='About using NCBI resources with assistive technology'>Accessibility</a> |
+      <a href='http://www.ncbi.nlm.nih.gov/About/glance/contact_info.html'
+      title='How to get help, submit data, or provide feedback'>Contact</a> |
+      <a href='mailto:blast-help@ncbi.nlm.nih.gov'
+      title='How to get help, submit data, or provide feedback'>Send feedback</a>      
+   </p>
+</div>	
+   </div><!--/#wrap-->
+</body>
+
+</html>

data/spec/fixtures/rid_response.html

@@ -0,0 +1,553 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<meta name="jig" content="ncbitoggler ncbiautocomplete"/>
+<meta name="ncbi_app" content="blast" />
+<meta name="ncbi_pdid" content="blastformatreq" />
+<meta name="ncbi_stat" content="false" />
+<meta name="ncbi_sessionid" content="5AAB767C0BD330A1_0000SID" />
+<meta name="ncbi_phid" content="5AAB767C0BD330A100000000000008B6" />
+<script type="text/javascript"> var ncbi_startTime = new Date(); </script>
+<title>NCBI Blast</title>
+<link rel="stylesheet" type="text/css" href="css/main.css" media="screen" />
+<link rel="stylesheet" type="text/css" href="css/common.css" media="screen" />
+<link rel="stylesheet" type="text/css" href="css/blastReq.css" media="screen" />
+<!--[if IE]>
+<link rel="stylesheet" type="text/css" href="css/blastReqIE.css" media="screen" />
+<![endif]-->
+<link rel="stylesheet" type="text/css" href="css/print.css" media="print" />
+
+
+<!--[if lte IE 6]>
+<link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
+<![endif]-->
+<script type="text/javascript" src="http://www.ncbi.nlm.nih.gov/core/jig/1.11/js/jig.min.js"></script>   
+<script type="text/javascript" src="js/utils.js"></script>
+<script type="text/javascript" src="js/blast.js"></script>
+<script type="text/javascript" src="js/format.js"></script>
+
+</head>
+
+<body id="type-a">
+
+<div id="wrap">
+			<div id="header">	    
+		<div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov" title="NCBI Home Page"><img src="css/images/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page" /></a>BLAST <span id="trdm"> &reg;</span><h1 class="desc">Basic Local Alignment Search Tool</h1>
+		</div>
+		<div id="search">
+		
+<div>
+<script language="JavaScript" type="text/javascript"><!--
+// --></script><table class="medium1" style="border:2px solid #336699;" cellpadding="2" cellspacing="0" id="myncbi_off"><tr><td
+bgcolor="#336699" align="left"><a href="http://www.ncbi.nlm.nih.gov/sites/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td
+bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img border="0"
+src="http://www.ncbi.nlm.nih.gov/corehtml/query/MyNCBI/myncbihelpicon.gif" alt="My NCBI help" /></a></td></tr><tr><td colspan="2" nowrap="nowrap"><a
+href="http://www.ncbi.nlm.nih.gov/sites/myncbi/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FCLIENT%3Dweb%2B%2B%2B%2B%26CMD%3DPut%26DATABASE%3Dnr%26ENTREZ%5FQUERY%3D%26EXPECT%3D10%26FILTER%3DL%2B%2B%2B%2B%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dnr%26HITLIST%5FSIZE%3D10%26JOB%5FTITLE%3Dgi%257C555%2B%2B%28624%2Bletters%29%26MYNCBI%5FUSER%3D7267509383%26MYNCBI%5FUSER%3D7267509383%26NCBI%5FGI%3Don%26PAGE%3DNucleotides%2B%2B%2B%2B%26PROGRAM%3Dblastn%26QUERY%5FINFO%3Dgi%257C555%2B%2B%28624%2Bletters%29%26QUERY%5FLENGTH%3D624%26RID%3DBUCSAKD101R%26RTOE%3D17%26SERVICE%3Dplain%26USER%5FTYPE%3D2%26USER%5FTYPE%3D2" title="Click to sign in"
+onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/sites/myncbi/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FCLIENT%3Dweb%2B%2B%2B%2B%26CMD%3DPut%26DATABASE%3Dnr%26ENTREZ%5FQUERY%3D%26EXPECT%3D10%26FILTER%3DL%2B%2B%2B%2B%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dnr%26HITLIST%5FSIZE%3D10%26JOB%5FTITLE%3Dgi%257C555%2B%2B%28624%2Bletters%29%26MYNCBI%5FUSER%3D7267509383%26MYNCBI%5FUSER%3D7267509383%26NCBI%5FGI%3Don%26PAGE%3DNucleotides%2B%2B%2B%2B%26PROGRAM%3Dblastn%26QUERY%5FINFO%3Dgi%257C555%2B%2B%28624%2Bletters%29%26QUERY%5FLENGTH%3D624%26RID%3DBUCSAKD101R%26RTOE%3D17%26SERVICE%3Dplain%26USER%5FTYPE%3D2%26USER%5FTYPE%3D2');return false;">[Sign In]</a> <a
+href="http://www.ncbi.nlm.nih.gov/sites/myncbi/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FCLIENT%3Dweb%2B%2B%2B%2B%26CMD%3DPut%26DATABASE%3Dnr%26ENTREZ%5FQUERY%3D%26EXPECT%3D10%26FILTER%3DL%2B%2B%2B%2B%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dnr%26HITLIST%5FSIZE%3D10%26JOB%5FTITLE%3Dgi%257C555%2B%2B%28624%2Bletters%29%26MYNCBI%5FUSER%3D7267509383%26MYNCBI%5FUSER%3D7267509383%26NCBI%5FGI%3Don%26PAGE%3DNucleotides%2B%2B%2B%2B%26PROGRAM%3Dblastn%26QUERY%5FINFO%3Dgi%257C555%2B%2B%28624%2Bletters%29%26QUERY%5FLENGTH%3D624%26RID%3DBUCSAKD101R%26RTOE%3D17%26SERVICE%3Dplain%26USER%5FTYPE%3D2%26USER%5FTYPE%3D2" title="Click to register for an account"
+onclick="MyNCBI_auto_submit('http://www.ncbi.nlm.nih.gov/sites/myncbi/register/?back_url=http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3FCLIENT%3Dweb%2B%2B%2B%2B%26CMD%3DPut%26DATABASE%3Dnr%26ENTREZ%5FQUERY%3D%26EXPECT%3D10%26FILTER%3DL%2B%2B%2B%2B%26FORMAT%5FTYPE%3DHTML%26FULL%5FDBNAME%3Dnr%26HITLIST%5FSIZE%3D10%26JOB%5FTITLE%3Dgi%257C555%2B%2B%28624%2Bletters%29%26MYNCBI%5FUSER%3D7267509383%26MYNCBI%5FUSER%3D7267509383%26NCBI%5FGI%3Don%26PAGE%3DNucleotides%2B%2B%2B%2B%26PROGRAM%3Dblastn%26QUERY%5FINFO%3Dgi%257C555%2B%2B%28624%2Bletters%29%26QUERY%5FLENGTH%3D624%26RID%3DBUCSAKD101R%26RTOE%3D17%26SERVICE%3Dplain%26USER%5FTYPE%3D2%26USER%5FTYPE%3D2');return false;">[Register]</a></td></tr></table></div>
+		</div>
+		<a class="skp" href="#content-wrap">Jump to Page Content</a>		
+		<ul id="nav">
+                <li  class="first "><a href="Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
+                <li  class="recent "><a href="Blast.cgi?CMD=GetSaved&amp;RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li>                
+                <li  class="saved "><a href="Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST search parameters">Saved Strategies</a></li>
+                <li  class= "last documentation "> <a href="Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs" title="BLAST documentation">Help</a></li>                
+                </ul>
+    </div>
+        <div id="content-wrap">
+
+                <!-- %%% Add breadcrumb text -->
+                <div id="breadcrumb">
+                   <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/
+                   <a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST</a>/                   
+                   <strong>Format Request</strong>
+                   <span id="frmRequestPrTr"></span>                   
+                </div>
+
+				<!-- Do errors this way -->				
+				<!--<ul class="msg"><li class=""><p></p></li></ul>-->
+				<ul id="msgR" class="msg"><li class=""></li></ul>
+                <div id="content">
+				<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="FormatForm" id="FormatForm">				
+
+<script language="JavaScript">
+
+ <!--
+
+//document.images['BlastHeaderGif'].src = 'html/head_formating.gif';
+
+// -->
+
+</script>
+
+
+
+<!--
+                <p class='info'>
+<strong>Job submitted.</strong>
+We estimate that results will be ready in 16 seconds or less.
+
+</p>
+-->
+
+<div class="fbtn">
+<!--
+<a href="javascript:document.forms[0].submit();">
+<img align="middle" alt="Format button" border="0" src="FormatPage_files/format_but.gif">
+</a>
+-->
+</div>
+
+<dl class="summary  query title db">
+<dd>
+</dd>
+
+<!-- <span class=" query title db">-->
+<!-- <span  class="hidden query"><dt>Query</dt><dd>gi|555  (624 letters)</dd></span> -->
+<dt class="hidden query">Query</dt><dd class="hidden query">gi|555  (624 letters)</dd>
+<dt class="hidden db">Database</dt><dd class="hidden db">nr</dd>
+<dt class="hidden title">Job title</dt><dd class="hidden title">gi|555  (624 letters)</dd>
+<dt class="hidden entrez">Entrez Query</dt><dd class="hidden entrez"><span class="note entrez">Note: Your search is limited to records matching this Entrez query</span></dd>
+<!-- </span> -->
+<dt><label for="rid">Request ID</label></dt><dd><input name="RID" size="50" type="text" value="BUCSAKD101R" id="rid" />
+<input type="submit" value="View report" name="ViewReport" class="button" />
+<!-- <img border="0" id="viewRpButton" src="images/veiwRpButton.jpg" class="viewReport"  alt="View report"  mouseovImg="images/veiwRpButtonOver.jpg" mouseoutImg="images/veiwRpButton.jpg" mousedownImg="images/veiwRpButtonDown.jpg" mouseupImg="images/veiwRpButtonOver.jpg"  />-->
+<input type="checkbox" name="NEWWINRES"  form="FormatForm" winType="const" id="nw" class="newwin"  />
+<label for="nw">Show results in a new window</label>
+</dd>
+<dt>Format<br/>
+<!--<a class='help' href="#">[Help]</a></dt> -->
+
+<dd>
+<table class="options blastn ">
+
+<tr class="paramSet xgl">
+<td class="hd"><label for="FORMAT_OBJECT">Show</label></td>
+<td>
+<div class="fi">
+<select id="FORMAT_OBJECT" class="reset" name="FORMAT_OBJECT" defVal="Alignment">
+<option value="Alignment" >Alignment</option>
+<option value="PSSM_Scoremat" >PssmWithParameters</option>
+<option value="Bioseq"  >Bioseq</option>
+</select>
+<label for="FORMAT_TYPE">as</label>
+<select name="FORMAT_TYPE" id="FORMAT_TYPE" class="reset" defVal="HTML">
+<option value="HTML" selected="selected" >HTML</option>
+<option value="Text"  >Plain text</option>
+<option value="ASN.1"  >ASN.1</option>
+<option value="XML"  >XML</option>
+</select>
+<input name="PSSM_FORMAT_TYPE" value="Text" size="3" id="pssmFormat" type="text" class="hidden dispType" />
+<input name="BIOSEQ_FORMAT_TYPE" value="ASN.1" size="3" id="bioseqFormat" type="text" class="hidden dispType" />
+<input name="PSSM_SC_FORMAT_TYPE" value="ASN.1" size="3" id="pssmScFormat" type="text" class="hidden dispType" />
+<span id="advView" class="">
+<span class=""><input name="OLD_VIEW" id="OLD_VIEW" type="checkbox" class="cb reset" defVal="checked"  />
+<label for="OLD_VIEW">Old View</label></span>
+</span>
+<a class="resetAll" id="resetAll" >Reset form to defaults</a>
+<a class="helplink  jig-ncbitoggler ui-ncbitoggler" title="Alignments object formatting help" id="formatHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive" >
+<p class="helpbox ui-ncbitoggler-slave" id="hlp1">
+These options control formatting of alignments in results pages. The
+default is HTML, but other formats (including plain text) are available.
+PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST. 
+The Advanced view option allows the database descriptions to be sorted by various indices in a table.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#format_object" target="helpWin" title="Additional alignments object formatting help">more...</a>
+</p>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+<tr class="odd paramSet">
+<td class="hd"><label for="ALIGNMENT_VIEW">Alignment View</label></td>
+<td>
+<div class="fi">
+<select name="ALIGNMENT_VIEW" id="ALIGNMENT_VIEW" defVal="Pairwise" class="reset">
+<option value="Pairwise"  >Pairwise</option>
+<option value="PairwiseWithIdentities"  >Pairwise with dots for identities</option>
+<option value="QueryAnchored"  >Query-anchored with dots for identities</option>
+<option value="QueryAnchoredNoIdentities"  >Query-anchored with letters for identities</option>
+<option value="FlatQueryAnchored"  >Flat query-anchored with dots for identities</option>
+<option value="FlatQueryAnchoredNoIdentities"  >Flat query-anchored with letters for identities</option>
+<option value="Tabular"  >Hit Table</option>
+</select>
+
+<a class="helplink  jig-ncbitoggler ui-ncbitoggler" title="Alignments view options help" id="alnViewHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive" >
+<p class="helpbox ui-ncbitoggler-slave" id="hlp2">
+Choose how to view alignments.
+The default "pairwise" view shows how each subject sequence aligns
+individually to the query sequence. The "query-anchored" view shows how
+all subject sequences align to the query sequence. For each view type,
+you can choose to show "identities" (matching residues) as letters or
+dots.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#alignment_view" target="helpWin" title="Additional alignments view options help">more...</a>
+</p>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+<tr class="paramSet">
+<td class="hd"><label>Display</label></td>
+<td class="cb">
+<div class="fi">
+<input name="SHOW_OVERVIEW" id="SHOW_OVERVIEW" type="checkbox" class="cb reset" defVal="checked" checked="checked" />
+<label class="rb" for="SHOW_OVERVIEW">Graphical Overview</label>
+
+<span id="shl" >
+<input name="SHOW_LINKOUT" id="SHOW_LINKOUT" type="checkbox" class="cb reset" defVal="checked" checked="checked" />
+<label class="rb" for="SHOW_LINKOUT">Linkout</label>
+</span>
+<span id="gts" >
+<input name="GET_SEQUENCE" id="GET_SEQUENCE" type="checkbox" class="cb reset" defVal="checked" checked="checked" />
+<label class="rb" for="GET_SEQUENCE">Sequence Retrieval</label>
+</span>
+
+<input name="NCBI_GI" id="NCBI_GI" type="checkbox" class="cb reset" defVal="unchecked" checked="checked" />
+<label class="rb" for="NCBI_GI">NCBI-gi</label>
+<span id="scf" >
+<input name="SHOW_CDS_FEATURE" id="SHOW_CDS_FEATURE" type="checkbox" class="cb reset blastn" defVal="unchecked"  />
+<label for="SHOW_CDS_FEATURE" class="blastn">CDS feature</label>
+</span>
+<a class="helplink  jig-ncbitoggler ui-ncbitoggler" title="Alignments display options help" id="displayHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive" >
+<ul class="helpbox ui-ncbitoggler-slave" id="hlp3">
+<li>Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to  query.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_overview" target="helpWin" title="Graphical Overview help">more...</a>
+</li>
+<li>Database LinkOuts: Show links from matching sequences to entries in specialized NCBI databases.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_linkout" title="LinkOut help" target="helpWin" >more...</a>
+</li>
+<li>Sequence Retrieval: Show buttons to download matching sequences.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#get_sequence" title="Sequence Retrieval help" target="helpWin" >more...</a>
+</li>
+<li>NCBI-gi: Show NCBI gi identifiers.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#ncbi_gi" title="NCBI-gi help" target="helpWin" >more...</a>
+</li>
+<li>CDS feature: Show annotated coding region and translation.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_cds_feature" title="CDS feature help" target="helpWin" >more...</a>
+</li></ul>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+
+<tr class="paramSet odd xgl">
+<td class="hd"><label>Masking</label></td>
+<td>
+<div class="fi">
+<label for="MASK_CHAR"> Character: </label>
+<select name="MASK_CHAR" id="MASK_CHAR"  class="reset" defVal="2">
+<option value="0"  >X for protein, n for nucleotide</option>
+<option value="2" selected="selected" >Lower Case</option>
+</select>
+<label for="MASK_COLOR"> Color:</label>
+<select name="MASK_COLOR" id="MASK_COLOR" class="reset" defVal="1">
+<option value="0"  >Black
+</option>
+
+<option value="1" selected="selected" >Grey
+</option>
+
+<option value="2"  >Red
+</option>
+
+</select>
+<a class="helplink  jig-ncbitoggler ui-ncbitoggler" title="Alignments masking help" id="maskingHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive" >
+<ul class="helpbox ui-ncbitoggler-slave" id="hlp4">
+<li>Masking Character: Display masked (filtered) sequence regions as lower-case or as specific letters (N for nucleotide, P for protein).
+</li>
+<li>Masking Color: Display masked sequence regions in the given color.</li>
+</ul>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+
+<tr class="paramSet xgl">
+<td class="hd"><label>Limit results</label></td>
+<td>
+<div class="fi">
+<label for="FRM_DESCRIPTIONS">Descriptions:</label>
+<select name="DESCRIPTIONS" id="FRM_DESCRIPTIONS" class="reset" defVal="100">
+<option value="0"      >0</option>
+<option value="10"     >10</option>
+<option value="50"     >50</option>
+<option value="100"   selected="selected" >100</option>
+<option value="250"    >250</option>
+<option value="500"    >500</option>
+<option value="1000"   >1000</option>
+<option value="5000"   >5000</option>
+<option value="10000"  >10000</option>
+<option value="20000"  >20000</option>
+</select>
+
+<label for="FRM_NUM_OVERVIEW">Graphical overview:</label>
+<select name="NUM_OVERVIEW" id="FRM_NUM_OVERVIEW" class="reset" defVal="100">
+<option value="0"     >0</option>
+<option value="10"    >10</option>
+<option value="50"    >50</option>
+<option value="100"  selected="selected" >100</option>
+<option value="250"   >250</option>
+<option value="500"  >500</option>
+<option value="1000"  >1000</option>
+</select>
+<span id="frmAln">
+<label for="FRM_ALIGNMENTS">Alignments:</label>
+<select name="ALIGNMENTS" id="FRM_ALIGNMENTS" class="reset" defVal="100">
+<option value="0"      >0</option>
+<option value="10"     >10</option>
+<option value="50"     >50</option>
+<option value="100"   selected="selected" >100</option>
+<option value="250"    >250</option>
+<option value="500"    >500</option>
+<option value="1000"   >1000</option>
+<option value="5000"   >5000</option>
+<option value="10000"  >10000</option>
+<option value="20000"  >20000</option>
+</select>
+</span>
+<a class="helplink  jig-ncbitoggler ui-ncbitoggler" title="Limit number of descriptions/alignments help" id="numHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive" >
+<ul class="helpbox ui-ncbitoggler-slave" id="hlp5">
+<li>Descriptions: Show short descriptions for up to the given number of  sequences.</li> 
+<li>Alignments:  Show alignments for up to the given number of sequences, in order of statistical significance.</li>
+</ul>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+<tr class="paramSet odd xgl">
+<td class="hd"></td>
+<td>
+<div class="">
+<label for="qorganism">Organism</label>
+<span class="instr">Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown.</span><br>
+<input name="FORMAT_ORGANISM" size="55"  type="text" id="qorganism" value="" data-jigconfig="dictionary:'taxids_sg'" autocomplete="off" class="jig-ncbiautocomplete reset">
+<input type="checkbox" name="FORMAT_ORG_EXCLUDE"  class="oExclR cb" id="orgExcl"/>        
+<input type="hidden" value = "1" name="FORMAT_NUM_ORG" id="numOrg" />
+<label for="orgExcl" class="right">Exclude</label>
+<a href="#" title="Add organism" id="addOrg"><img border="0" src="css/images/addOrg.jpg" id="addOrgIm"   alt="Add organism"  mouseovImg="css/images/addOrgOver.jpg" mouseoutImg="css/images/addOrg.jpg" mousedownImg="css/images/addOrgDown.jpg" mouseupImg="css/images/addOrgOver.jpg"  /></a>
+<div id="orgs">
+
+</div>
+<div class="fi">
+<a class="helplink  jig-ncbitoggler ui-ncbitoggler" title="Limit results by organism help" id="organismHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive" >
+<p class="helpbox ui-ncbitoggler-slave" id="hlp6">
+Show only sequences from the given organism.
+</p>
+</div><!-- ARIA -->
+</div>
+</div>
+</td>
+</tr>
+
+<tr class="paramSet xgl">
+<td class="hd"></td>
+<td>
+<div class="fi">
+<label for="FORMAT_EQ_TEXT">Entrez query:</label>
+<input name="FORMAT_EQ_TEXT" id="FORMAT_EQ_TEXT" size="60" type="text" value="" class="reset" />
+<a class="helplink  jig-ncbitoggler ui-ncbitoggler" title="Limit results by Entrez query help" id="entrezHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive" >
+<p class="helpbox ui-ncbitoggler-slave" id="hlp7">
+Show only those sequences that match the given Entrez query.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#limit_result" target="helpWin" title="Additional limit results by Entrez query help"  target="helpWin">more...</a>
+</p>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+
+  
+<tr class="paramSet odd xgl">
+<td class="hd"></td>
+<td>
+<div class="fi">
+<label for="EXPECT_LOW">Expect Min:</label> <input name="EXPECT_LOW" id="EXPECT_LOW" size="10" type="text" value="" class="reset"/>
+<label for="EXPECT_HIGH">Expect Max:</label> <input name="EXPECT_HIGH" id="EXPECT_HIGH" size="10" type="text" value="" class="reset" />
+<a class="helplink  jig-ncbitoggler ui-ncbitoggler" title="Limit results by expect value range help" id="expectHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive" >
+<p class="helpbox ui-ncbitoggler-slave" id="hlp8">
+Show only sequences with expect values in the given range.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#expect_range" target="helpWin" title="Additional limit results by expect value range help">more...</a>
+</p>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+<tr class="paramSet xgl">
+<td class="hd"></td>
+<td>
+ <div class="fi">
+<label for="PERC_IDENT_LOW">Percent Identity Min:</label> <input name="PERC_IDENT_LOW" id="PERC_IDENT_LOW" size="10" type="text" value="" class="reset"/>
+<label for="PERC_IDENT_HIGH">Percent Identity Max:</label> <input name="PERC_IDENT_HIGH" id="PERC_IDENT_HIGH" size="10" type="text" value="" class="reset" />
+<a class="helplink  jig-ncbitoggler ui-ncbitoggler" title="Limit results by percent identity range help" id="percIdentHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive" >
+<p class="helpbox ui-ncbitoggler-slave" id="hlp10">
+ Show only sequences with percent identity values in the given range.  
+</p>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>      
+<tr class="psiBlast odd paramSet xgl">
+<td class="hd"><label>Format for</label></td>
+<td>
+<div class="fi">
+<input name="RUN_PSIBLAST_FORM" id="RUN_PSIBLAST" type="checkbox" class="cb psiBlast"  />
+<label class="rb psiBlast" for="RUN_PSIBLAST">PSI-BLAST</label>
+<label for="I_THRESH">with inclusion threshold:</label>
+<input name="I_THRESH" id="I_THRESH" size="10" type="text" value="" defVal="0.005" />
+<a class="helplink  jig-ncbitoggler ui-ncbitoggler" title="PSI BLAST formatting help" id="psiHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
+<span class="ui-icon ui-icon-triangle-1-e"></span></a>
+<div class="ui-helper-reset" aria-live="assertive" >
+<ul class="helpbox ui-ncbitoggler-slave" id="hlp9">
+<li>Format for PSI-BLAST: The Position-Specific Iterated BLAST (PSI-BLAST) program performs iterative searches with a protein query, 
+in which sequences found in one round of search are used to build a custom score model for the next round.
+<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#psiblast" target="helpWin" title="Additional PSI BLAST formatting help">more...</a>
+</li>  
+<li>Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used 
+by PSI-BLAST to create the PSSM on the next iteration.</li> 
+</ul>
+</div><!-- ARIA -->
+</div>
+</td>
+</tr>
+</table>
+</dd>
+</dl>
+
+<input name="RID" value="BUCSAKD101R" type="hidden" />
+<input name="CDD_RID" value="" type="hidden" />
+<input name="CDD_SEARCH_STATE" type="hidden" value="" />
+
+<input name="STEP_NUMBER" value="" id="stepNumber" type="hidden" />
+<input name="CMD" value="Get" type="hidden" />
+<input name="FORMAT_EQ_OP" value="AND" type="hidden" />
+<input name="RESULTS_PAGE_TARGET" type="hidden" id="resPageTarget" value="Blast_Results_for_2041855348" />
+<input name="QUERY_INFO" type="hidden" value="gi|555  (624 letters)" />                   		
+
+<input name="ENTREZ_QUERY" type="hidden" value="" />
+<input name="QUERY_INDEX" type="hidden" value="0"/>
+<input name="NUM_QUERIES" type="hidden" value="1"/>
+<input name="CONFIG_DESCR" type="hidden" value="2,3,4,5,6,7,8" />
+
+<!-- Those params are set in the template (blastn.dat, blastp.dat etc. -->
+<input name="BLAST_PROGRAMS" type="hidden" value="blastn"/>
+<input name="PAGE" type="hidden" value="Nucleotides"/>
+<input name="PROGRAM" type="hidden" value="blastn"/>
+<input name="MEGABLAST" type="hidden" value="" />
+<input name="RUN_PSIBLAST" type="hidden" value="" />
+<input name="BLAST_SPEC" id="blastSpec" type="hidden" value=""/>
+
+
+<input name="QUERY" type="hidden" value=""/>
+<input name="JOB_TITLE" type="hidden" value="gi|555  (624 letters)"/>
+<input name="QUERY_TO" type="hidden" value=""/>
+<input name="QUERY_FROM" type="hidden" value=""/>
+<input name="EQ_TEXT" type="hidden" value=""/>
+<input name="ORGN" type="hidden" value=""/>
+<input name="EQ_MENU" type="hidden" value=""/>
+<input name="ORG_EXCLUDE" type="hidden" value=""/>
+<input name="PHI_PATTERN" type="hidden" value=""/>
+<input name="EXPECT" type="hidden" value="10"/>									
+<input name="DATABASE" type="hidden" value="nr"/>
+<input name="DB_GROUP" type="hidden" value=""/>
+<input name="SUBGROUP_NAME" type="hidden" value=""/>
+
+<input name="GENETIC_CODE" type="hidden" value=""/>
+<input name="WORD_SIZE" type="hidden" value=""/>
+<input name="MATCH_SCORES" type="hidden" value=""/>			
+<input name="MATRIX_NAME" type="hidden" value=""/>				
+<input name="GAPCOSTS" type="hidden" value=""/>
+<input name="MAX_NUM_SEQ" id="maxNumSeq" type="hidden" value=""/>					
+
+<input name="COMPOSITION_BASED_STATISTICS" type="hidden" value=""/>			
+<input name="NEWWIN" type="hidden" value=""/>
+<input name="SHORT_QUERY_ADJUST" type="hidden" value=""/>
+<input name="FILTER" type="hidden" value="L    ;"/>
+<input name="REPEATS" type="hidden" value=""/>
+<input name="ID_FOR_PSSM" type="hidden" value=""/>
+<input name="EXCLUDE_MODELS" type="hidden" value=""/>
+<input name="EXCLUDE_SEQ_UNCULT" type="hidden" value=""/>
+<input name="NUM_ORG" type="hidden" value = "1" />
+
+<!-- PSSM -->
+<input name="LCASE_MASK" type="hidden" value=""/>
+<input name="TEMPLATE_TYPE" type="hidden" value=""/>
+<input name="TEMPLATE_LENGTH" type="hidden" value=""/>
+<input name="I_THRESH" type="hidden" value=""/>
+<input name="PSI_PSEUDOCOUNT" type="hidden" value=""/>
+<input name="DI_THRESH" type="hidden" id="diThresh" value=""/>
+<input name="HSP_RANGE_MAX" type="hidden" value=""/>
+
+
+
+<input name="ADJUSTED_FOR_SHORT_QUERY" type="hidden" value=""/>
+<input name="MIXED_QUERIES" type="hidden" value=""/>
+<input name="MIXED_DATABASE" id="mixedDb" type="hidden" value=""/>
+<input name="BUILD_NAME"  type="hidden" value=""/>
+<input name="ORG_DBS"  type="hidden" value=""/>
+
+<!--QBlastInfoBegin
+    RID = BUCSAKD101R
+    RTOE = 17
+QBlastInfoEnd
+-->
+</form>		                              		
+				
+				</div><!-- /#content -->
+
+        </div><!-- /#content-wrap -->
+
+		    	
+<div id="footer">
+   <div id="rgs">BLAST is a registered trademark of the National Library of Medicine.</div> 
+   <p id="orgns">
+      <a href="http://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information">NCBI</a> |
+      <a href="http://www.nlm.nih.gov/" title="National Library of Medicine">NLM</a> |
+      <a href="http://www.nih.gov/" title="National Institutes of Health">NIH</a> |
+      <a href="http://www.hhs.gov/" title="US Department of Health and Human Services">DHHS</a>
+   </p>
+   
+   <p>
+      <a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html'
+      title='NCBI intellectual property statement'>Copyright</a> | 
+      <a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html#disclaimer'
+      title='About liability, endorsements, external links, pop-up advertisements'>Disclaimer</a> | 
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+      <a href='http://www.ncbi.nlm.nih.gov/About/glance/contact_info.html'
+      title='How to get help, submit data, or provide feedback'>Contact</a> |
+      <a href='mailto:blast-help@ncbi.nlm.nih.gov'
+      title='How to get help, submit data, or provide feedback'>Send feedback</a>      
+   </p>
+</div>	
+   </div><!--/#wrap-->
+
+<script type="text/javascript" src="http://blast.ncbi.nlm.nih.gov/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js"></script>
+</body>
+
+</html>
+