ncbi_blast_results_parser 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.gitignore +17 -0
- data/Gemfile +3 -0
- data/LICENCE +20 -0
- data/README.md +30 -0
- data/Rakefile +8 -0
- data/lib/ncbi_blast_results_parser.rb +39 -0
- data/lib/ncbi_blast_results_parser/rid_parser.rb +22 -0
- data/lib/ncbi_blast_results_parser/status_parser.rb +15 -0
- data/lib/ncbi_blast_results_parser/version.rb +3 -0
- data/ncbi_blast_results_parser.gemspec +25 -0
- data/spec/fixtures/ready_response.html +135 -0
- data/spec/fixtures/rid_response.html +553 -0
- data/spec/fixtures/unknown_response.html +135 -0
- data/spec/fixtures/waiting_response.html +135 -0
- data/spec/lib/ncbi_blast_results_parser/rid_parser_spec.rb +22 -0
- data/spec/lib/ncbi_blast_results_parser/status_parser_spec.rb +29 -0
- data/spec/lib/ncbi_blast_results_parser_spec.rb +24 -0
- data/spec/spec_helper.rb +8 -0
- metadata +115 -0
data/.gitignore
ADDED
data/Gemfile
ADDED
data/LICENCE
ADDED
@@ -0,0 +1,20 @@
|
|
1
|
+
Copyright (c) 2013 Gareth Rees & Angharad Williams
|
2
|
+
|
3
|
+
Permission is hereby granted, free of charge, to any person obtaining
|
4
|
+
a copy of this software and associated documentation files (the
|
5
|
+
"Software"), to deal in the Software without restriction, including
|
6
|
+
without limitation the rights to use, copy, modify, merge, publish,
|
7
|
+
distribute, sublicense, and/or sell copies of the Software, and to
|
8
|
+
permit persons to whom the Software is furnished to do so, subject to
|
9
|
+
the following conditions:
|
10
|
+
|
11
|
+
The above copyright notice and this permission notice shall be
|
12
|
+
included in all copies or substantial portions of the Software.
|
13
|
+
|
14
|
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
15
|
+
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
|
16
|
+
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
17
|
+
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
|
18
|
+
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
|
19
|
+
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
|
20
|
+
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
data/README.md
ADDED
@@ -0,0 +1,30 @@
|
|
1
|
+
# NCBI Blast Results Parser
|
2
|
+
|
3
|
+
Parses useful information from the HTML response of an NCBI Blast.
|
4
|
+
|
5
|
+
## Current Methods
|
6
|
+
|
7
|
+
- `rid`: Parses a Request ID
|
8
|
+
- `wait`: Parses the suggested wait time before attempting to get results
|
9
|
+
- `status`: Parses the status of a Blast
|
10
|
+
|
11
|
+
## Usage
|
12
|
+
|
13
|
+
```ruby
|
14
|
+
rid = NCBIBlastResultsParser.rid(response)
|
15
|
+
#=> 'ABCD1234'
|
16
|
+
|
17
|
+
wait = NCBIBlastResultsParser.wait(response)
|
18
|
+
#=> 17
|
19
|
+
|
20
|
+
status = NCBIBlastResultsParser.status(response)
|
21
|
+
#=> 'READY'
|
22
|
+
```
|
23
|
+
|
24
|
+
## Contributing
|
25
|
+
|
26
|
+
1. Fork it
|
27
|
+
2. Create your feature branch (`git checkout -b my-new-feature`)
|
28
|
+
3. Commit your changes (`git commit -am 'Add some feature'`)
|
29
|
+
4. Push to the branch (`git push origin my-new-feature`)
|
30
|
+
5. Create new Pull Request
|
data/Rakefile
ADDED
@@ -0,0 +1,39 @@
|
|
1
|
+
require 'nokogiri'
|
2
|
+
|
3
|
+
Dir[File.dirname(__FILE__) + '/ncbi_blast_results_parser/*.rb'].each do |file|
|
4
|
+
require file
|
5
|
+
end
|
6
|
+
|
7
|
+
module NCBIBlastResultsParser
|
8
|
+
|
9
|
+
# Parse a Request ID from an NCBI Blast
|
10
|
+
#
|
11
|
+
# Returns a String
|
12
|
+
def self.rid(response)
|
13
|
+
rid_parser = NCBIBlastResultsParser::RIDParser.new
|
14
|
+
parser = Nokogiri::HTML::SAX::Parser.new(rid_parser)
|
15
|
+
parser.parse(response)
|
16
|
+
rid_parser.rid
|
17
|
+
end
|
18
|
+
|
19
|
+
# Parse the suggested wait time for an NCBI Blast
|
20
|
+
#
|
21
|
+
# Returns an Integer
|
22
|
+
def self.wait(response)
|
23
|
+
rid_parser = NCBIBlastResultsParser::RIDParser.new
|
24
|
+
parser = Nokogiri::HTML::SAX::Parser.new(rid_parser)
|
25
|
+
parser.parse(response)
|
26
|
+
rid_parser.wait
|
27
|
+
end
|
28
|
+
|
29
|
+
# Parse the status from an NCBI Blast
|
30
|
+
#
|
31
|
+
# Returns a String
|
32
|
+
def self.status(response)
|
33
|
+
status_parser = NCBIBlastResultsParser::StatusParser.new
|
34
|
+
parser = Nokogiri::HTML::SAX::Parser.new(status_parser)
|
35
|
+
parser.parse(response)
|
36
|
+
status_parser.status
|
37
|
+
end
|
38
|
+
|
39
|
+
end
|
@@ -0,0 +1,22 @@
|
|
1
|
+
module NCBIBlastResultsParser
|
2
|
+
class RIDParser < Nokogiri::XML::SAX::Document
|
3
|
+
|
4
|
+
attr_reader :rid, :wait
|
5
|
+
|
6
|
+
def comment(string)
|
7
|
+
parse_rid(string) if string.strip.include? 'RID ='
|
8
|
+
parse_wait_time(string) if string.strip.include? 'RTOE ='
|
9
|
+
end
|
10
|
+
|
11
|
+
def parse_rid(string)
|
12
|
+
line = string[/((?:RID =.*?$){1})/]
|
13
|
+
@rid = line.split.last
|
14
|
+
end
|
15
|
+
|
16
|
+
def parse_wait_time(string)
|
17
|
+
line = string[/((?:RTOE =.*?$){1})/]
|
18
|
+
@wait = line.split.last.to_i
|
19
|
+
end
|
20
|
+
|
21
|
+
end
|
22
|
+
end
|
@@ -0,0 +1,15 @@
|
|
1
|
+
module NCBIBlastResultsParser
|
2
|
+
class StatusParser < Nokogiri::XML::SAX::Document
|
3
|
+
|
4
|
+
attr_reader :status
|
5
|
+
|
6
|
+
def comment(string)
|
7
|
+
parse_status(string) if string.strip.include? 'Status='
|
8
|
+
end
|
9
|
+
|
10
|
+
def parse_status(string)
|
11
|
+
line = string[/((?:Status=.*?$){1})/]
|
12
|
+
@status = line.split('=').last
|
13
|
+
end
|
14
|
+
end
|
15
|
+
end
|
@@ -0,0 +1,25 @@
|
|
1
|
+
# -*- encoding: utf-8 -*-
|
2
|
+
lib = File.expand_path('../lib', __FILE__)
|
3
|
+
$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
|
4
|
+
require 'ncbi_blast_results_parser/version'
|
5
|
+
|
6
|
+
Gem::Specification.new do |gem|
|
7
|
+
gem.name = 'ncbi_blast_results_parser'
|
8
|
+
gem.version = NCBIBlastResultsParser::VERSION
|
9
|
+
gem.authors = ['Gareth Rees']
|
10
|
+
gem.email = ['gareth@garethrees.co.uk']
|
11
|
+
gem.description = %q{Parses useful information from the HTML response of an NCBI Blast}
|
12
|
+
gem.summary = %q{Parses useful information from the HTML response of an NCBI Blast}
|
13
|
+
gem.homepage = ''
|
14
|
+
|
15
|
+
gem.files = `git ls-files`.split($/)
|
16
|
+
gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
|
17
|
+
gem.test_files = gem.files.grep(%r{^(test|spec|features)/})
|
18
|
+
gem.require_paths = ['lib']
|
19
|
+
|
20
|
+
gem.add_dependency 'nokogiri'
|
21
|
+
|
22
|
+
gem.add_development_dependency 'minitest'
|
23
|
+
gem.add_development_dependency 'turn'
|
24
|
+
gem.add_development_dependency 'rake'
|
25
|
+
end
|
@@ -0,0 +1,135 @@
|
|
1
|
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
2
|
+
<html xmlns="http://www.w3.org/1999/xhtml">
|
3
|
+
<head>
|
4
|
+
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
|
5
|
+
<meta name="jig" content="ncbitoggler"/>
|
6
|
+
<meta name="ncbitoggler" content="animation:'none'"/>
|
7
|
+
<title>NCBI Blast:</title>
|
8
|
+
<script type="text/javascript" src="http://www.ncbi.nlm.nih.gov/core/jig/1.11/js/jig.min.js"></script>
|
9
|
+
<link rel="stylesheet" type="text/css" href="css/main.css" media="screen" />
|
10
|
+
<link rel="stylesheet" type="text/css" href="css/blastRes.css" media="screen" />
|
11
|
+
<link rel="stylesheet" type="text/css" href="css/print.css" media="print" />
|
12
|
+
<!--[if lte IE 6]>
|
13
|
+
<link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
|
14
|
+
<![endif]-->
|
15
|
+
<script type="text/javascript" src="js/utils.js"></script>
|
16
|
+
<script type="text/javascript" src="js/results.js"></script>
|
17
|
+
</head>
|
18
|
+
|
19
|
+
<body id="type-a" class="noToggleCheck" >
|
20
|
+
<div id="wrap">
|
21
|
+
<div id="header">
|
22
|
+
<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"> ®</span><h1 class="desc">Basic Local Alignment Search Tool</h1>
|
23
|
+
</div>
|
24
|
+
<div id="search">
|
25
|
+
|
26
|
+
<div>
|
27
|
+
<script language="JavaScript" type="text/javascript"><!--
|
28
|
+
// --></script><table class="medium1" style="border:2px solid #336699;" cellpadding="2" cellspacing="0" id="myncbi_off"><tr><td
|
29
|
+
bgcolor="#336699" align="left"><a href="http://www.ncbi.nlm.nih.gov/myncbi/?"><font color="#FFFFFF"><b>My NCBI</b></font></a></td><td
|
30
|
+
bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img border="0"
|
31
|
+
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
|
32
|
+
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"
|
33
|
+
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
|
34
|
+
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"
|
35
|
+
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>
|
36
|
+
</div>
|
37
|
+
<a class="skp" href="#content-wrap">Jump to Page Content</a>
|
38
|
+
<ul id="nav">
|
39
|
+
<li class="first "><a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
|
40
|
+
<li class="recent "><a href="Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li>
|
41
|
+
<li class="saved "><a href="Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST search parameters">Saved Strategies</a></li>
|
42
|
+
<li class= "last documentation "> <a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs" title="BLAST documentation">Help</a></li>
|
43
|
+
</ul>
|
44
|
+
</div>
|
45
|
+
|
46
|
+
<div id="content-wrap">
|
47
|
+
|
48
|
+
<div id="breadcrumb" class="inlineDiv">
|
49
|
+
<a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/
|
50
|
+
<a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST</a>/
|
51
|
+
<a href="Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=">blastn suite</a>/
|
52
|
+
<strong>Formatting Results - HZMF5DEN015</strong>
|
53
|
+
</div>
|
54
|
+
<div class="inlineDiv resHeader">
|
55
|
+
<a id="frmPage" class="WAITING" href="#" submitForm="reformat">[Formatting options] </a>
|
56
|
+
</div>
|
57
|
+
<h3 id="jtitle" >Job Title: </h3>
|
58
|
+
|
59
|
+
<div id="content">
|
60
|
+
<!--<ul id="msg" class="msg"><li class=""><p class=""></p><p class=""></p><p class=""></p></ul> -->
|
61
|
+
<ul id="msg" class="msg"><li class=""></li></ul>
|
62
|
+
<p><!--
|
63
|
+
QBlastInfoBegin
|
64
|
+
Status=READY
|
65
|
+
QBlastInfoEnd
|
66
|
+
--></p>
|
67
|
+
|
68
|
+
<SCRIPT LANGUAGE="JavaScript"><!--
|
69
|
+
var tm = "2000";
|
70
|
+
if (tm != "") {
|
71
|
+
setTimeout('document.forms[0].submit();',tm);
|
72
|
+
}
|
73
|
+
//--></SCRIPT>
|
74
|
+
<table id="statInfo" class="WAITING">
|
75
|
+
<tr><td>Request ID</td><td> <b>HZMF5DEN015</b></td></tr>
|
76
|
+
<tr class="odd"><td>Status</td><td>Searching</td></tr>
|
77
|
+
<tr><td>Submitted at</td><td>Sat Feb 16 13:37:25 2013</td></tr>
|
78
|
+
<tr class="odd"><td>Current time</td><td>Sat Feb 16 13:37:26 2013</td></tr>
|
79
|
+
<tr><td>Time since submission</td><td>00:00:01</td></tr>
|
80
|
+
</table>
|
81
|
+
<p class="WAITING">This page will be automatically updated in <b>2</b> seconds</p>
|
82
|
+
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST" id="results">
|
83
|
+
<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">
|
84
|
+
<input name="_PGR" type="hidden" value="0" >
|
85
|
+
<input name="CMD" type="hidden" value="Get">
|
86
|
+
|
87
|
+
</form>
|
88
|
+
|
89
|
+
</div><!-- /#content -->
|
90
|
+
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="reformat" id="reformat">
|
91
|
+
<input name="QUERY_INFO" type="hidden" value="" />
|
92
|
+
<input name="ENTREZ_QUERY" type="hidden" value="" />
|
93
|
+
<input name="CDD_RID" type="hidden" value="" />
|
94
|
+
<input name="CDD_SEARCH_STATE" type="hidden" value="" />
|
95
|
+
<input name="RID" type="hidden" value="HZMF5DEN015" />
|
96
|
+
<input name="STEP_NUMBER" type="hidden" value="" />
|
97
|
+
<input name="CMD" type="hidden" value="Web"/>
|
98
|
+
<input NAME="PAGE_TYPE" type="hidden" value="BlastFormatting"/>
|
99
|
+
|
100
|
+
<!-- TO DO: test all of those changes -->
|
101
|
+
<!-- Psi blast params PSI_BLAST_PARAMS - commented- using forms[0] from fromatter> -->
|
102
|
+
<!-- Current Formatting options FORMATTING_OPTIONS- commented- using forms[0] from fromatter> -->
|
103
|
+
<!-- Current Search options CURR_SAVED_OPTIONS - commented- using forms[0] from fromatter> -->
|
104
|
+
</form>
|
105
|
+
</div><!-- /#content-wrap -->
|
106
|
+
|
107
|
+
|
108
|
+
<div id="footer">
|
109
|
+
<div id="rgs">BLAST is a registered trademark of the National Library of Medicine.</div>
|
110
|
+
<p id="orgns">
|
111
|
+
<a href="http://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information">NCBI</a> |
|
112
|
+
<a href="http://www.nlm.nih.gov/" title="National Library of Medicine">NLM</a> |
|
113
|
+
<a href="http://www.nih.gov/" title="National Institutes of Health">NIH</a> |
|
114
|
+
<a href="http://www.hhs.gov/" title="US Department of Health and Human Services">DHHS</a>
|
115
|
+
</p>
|
116
|
+
|
117
|
+
<p>
|
118
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html'
|
119
|
+
title='NCBI intellectual property statement'>Copyright</a> |
|
120
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html#disclaimer'
|
121
|
+
title='About liability, endorsements, external links, pop-up advertisements'>Disclaimer</a> |
|
122
|
+
<a href='http://www.nlm.nih.gov/privacy.html'
|
123
|
+
title='NLM privacy policy'>Privacy</a> |
|
124
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/accessibility.html'
|
125
|
+
title='About using NCBI resources with assistive technology'>Accessibility</a> |
|
126
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/glance/contact_info.html'
|
127
|
+
title='How to get help, submit data, or provide feedback'>Contact</a> |
|
128
|
+
<a href='mailto:blast-help@ncbi.nlm.nih.gov'
|
129
|
+
title='How to get help, submit data, or provide feedback'>Send feedback</a>
|
130
|
+
</p>
|
131
|
+
</div>
|
132
|
+
</div><!--/#wrap-->
|
133
|
+
</body>
|
134
|
+
|
135
|
+
</html>
|
@@ -0,0 +1,553 @@
|
|
1
|
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
2
|
+
<html xmlns="http://www.w3.org/1999/xhtml">
|
3
|
+
<head>
|
4
|
+
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
|
5
|
+
<meta name="jig" content="ncbitoggler ncbiautocomplete"/>
|
6
|
+
<meta name="ncbi_app" content="blast" />
|
7
|
+
<meta name="ncbi_pdid" content="blastformatreq" />
|
8
|
+
<meta name="ncbi_stat" content="false" />
|
9
|
+
<meta name="ncbi_sessionid" content="5AAB767C0BD330A1_0000SID" />
|
10
|
+
<meta name="ncbi_phid" content="5AAB767C0BD330A100000000000008B6" />
|
11
|
+
<script type="text/javascript"> var ncbi_startTime = new Date(); </script>
|
12
|
+
<title>NCBI Blast</title>
|
13
|
+
<link rel="stylesheet" type="text/css" href="css/main.css" media="screen" />
|
14
|
+
<link rel="stylesheet" type="text/css" href="css/common.css" media="screen" />
|
15
|
+
<link rel="stylesheet" type="text/css" href="css/blastReq.css" media="screen" />
|
16
|
+
<!--[if IE]>
|
17
|
+
<link rel="stylesheet" type="text/css" href="css/blastReqIE.css" media="screen" />
|
18
|
+
<![endif]-->
|
19
|
+
<link rel="stylesheet" type="text/css" href="css/print.css" media="print" />
|
20
|
+
|
21
|
+
|
22
|
+
<!--[if lte IE 6]>
|
23
|
+
<link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
|
24
|
+
<![endif]-->
|
25
|
+
<script type="text/javascript" src="http://www.ncbi.nlm.nih.gov/core/jig/1.11/js/jig.min.js"></script>
|
26
|
+
<script type="text/javascript" src="js/utils.js"></script>
|
27
|
+
<script type="text/javascript" src="js/blast.js"></script>
|
28
|
+
<script type="text/javascript" src="js/format.js"></script>
|
29
|
+
|
30
|
+
</head>
|
31
|
+
|
32
|
+
<body id="type-a">
|
33
|
+
|
34
|
+
<div id="wrap">
|
35
|
+
<div id="header">
|
36
|
+
<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"> ®</span><h1 class="desc">Basic Local Alignment Search Tool</h1>
|
37
|
+
</div>
|
38
|
+
<div id="search">
|
39
|
+
|
40
|
+
<div>
|
41
|
+
<script language="JavaScript" type="text/javascript"><!--
|
42
|
+
// --></script><table class="medium1" style="border:2px solid #336699;" cellpadding="2" cellspacing="0" id="myncbi_off"><tr><td
|
43
|
+
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
|
44
|
+
bgcolor="#336699" align="right"><a href="http://www.ncbi.nlm.nih.gov/books/NBK3842/" title="My NCBI help"><img border="0"
|
45
|
+
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
|
46
|
+
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"
|
47
|
+
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
|
48
|
+
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"
|
49
|
+
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>
|
50
|
+
</div>
|
51
|
+
<a class="skp" href="#content-wrap">Jump to Page Content</a>
|
52
|
+
<ul id="nav">
|
53
|
+
<li class="first "><a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li>
|
54
|
+
<li class="recent "><a href="Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on" title="Unexpired BLAST jobs">Recent Results</a></li>
|
55
|
+
<li class="saved "><a href="Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST search parameters">Saved Strategies</a></li>
|
56
|
+
<li class= "last documentation "> <a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs" title="BLAST documentation">Help</a></li>
|
57
|
+
</ul>
|
58
|
+
</div>
|
59
|
+
<div id="content-wrap">
|
60
|
+
|
61
|
+
<!-- %%% Add breadcrumb text -->
|
62
|
+
<div id="breadcrumb">
|
63
|
+
<a href="http://www.ncbi.nlm.nih.gov/">NCBI</a>/
|
64
|
+
<a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST</a>/
|
65
|
+
<strong>Format Request</strong>
|
66
|
+
<span id="frmRequestPrTr"></span>
|
67
|
+
</div>
|
68
|
+
|
69
|
+
<!-- Do errors this way -->
|
70
|
+
<!--<ul class="msg"><li class=""><p></p></li></ul>-->
|
71
|
+
<ul id="msgR" class="msg"><li class=""></li></ul>
|
72
|
+
<div id="content">
|
73
|
+
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="post" name="FormatForm" id="FormatForm">
|
74
|
+
|
75
|
+
<script language="JavaScript">
|
76
|
+
|
77
|
+
<!--
|
78
|
+
|
79
|
+
//document.images['BlastHeaderGif'].src = 'html/head_formating.gif';
|
80
|
+
|
81
|
+
// -->
|
82
|
+
|
83
|
+
</script>
|
84
|
+
|
85
|
+
|
86
|
+
|
87
|
+
<!--
|
88
|
+
<p class='info'>
|
89
|
+
<strong>Job submitted.</strong>
|
90
|
+
We estimate that results will be ready in 16 seconds or less.
|
91
|
+
|
92
|
+
</p>
|
93
|
+
-->
|
94
|
+
|
95
|
+
<div class="fbtn">
|
96
|
+
<!--
|
97
|
+
<a href="javascript:document.forms[0].submit();">
|
98
|
+
<img align="middle" alt="Format button" border="0" src="FormatPage_files/format_but.gif">
|
99
|
+
</a>
|
100
|
+
-->
|
101
|
+
</div>
|
102
|
+
|
103
|
+
<dl class="summary query title db">
|
104
|
+
<dd>
|
105
|
+
</dd>
|
106
|
+
|
107
|
+
<!-- <span class=" query title db">-->
|
108
|
+
<!-- <span class="hidden query"><dt>Query</dt><dd>gi|555 (624 letters)</dd></span> -->
|
109
|
+
<dt class="hidden query">Query</dt><dd class="hidden query">gi|555 (624 letters)</dd>
|
110
|
+
<dt class="hidden db">Database</dt><dd class="hidden db">nr</dd>
|
111
|
+
<dt class="hidden title">Job title</dt><dd class="hidden title">gi|555 (624 letters)</dd>
|
112
|
+
<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>
|
113
|
+
<!-- </span> -->
|
114
|
+
<dt><label for="rid">Request ID</label></dt><dd><input name="RID" size="50" type="text" value="BUCSAKD101R" id="rid" />
|
115
|
+
<input type="submit" value="View report" name="ViewReport" class="button" />
|
116
|
+
<!-- <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" />-->
|
117
|
+
<input type="checkbox" name="NEWWINRES" form="FormatForm" winType="const" id="nw" class="newwin" />
|
118
|
+
<label for="nw">Show results in a new window</label>
|
119
|
+
</dd>
|
120
|
+
<dt>Format<br/>
|
121
|
+
<!--<a class='help' href="#">[Help]</a></dt> -->
|
122
|
+
|
123
|
+
<dd>
|
124
|
+
<table class="options blastn ">
|
125
|
+
|
126
|
+
<tr class="paramSet xgl">
|
127
|
+
<td class="hd"><label for="FORMAT_OBJECT">Show</label></td>
|
128
|
+
<td>
|
129
|
+
<div class="fi">
|
130
|
+
<select id="FORMAT_OBJECT" class="reset" name="FORMAT_OBJECT" defVal="Alignment">
|
131
|
+
<option value="Alignment" >Alignment</option>
|
132
|
+
<option value="PSSM_Scoremat" >PssmWithParameters</option>
|
133
|
+
<option value="Bioseq" >Bioseq</option>
|
134
|
+
</select>
|
135
|
+
<label for="FORMAT_TYPE">as</label>
|
136
|
+
<select name="FORMAT_TYPE" id="FORMAT_TYPE" class="reset" defVal="HTML">
|
137
|
+
<option value="HTML" selected="selected" >HTML</option>
|
138
|
+
<option value="Text" >Plain text</option>
|
139
|
+
<option value="ASN.1" >ASN.1</option>
|
140
|
+
<option value="XML" >XML</option>
|
141
|
+
</select>
|
142
|
+
<input name="PSSM_FORMAT_TYPE" value="Text" size="3" id="pssmFormat" type="text" class="hidden dispType" />
|
143
|
+
<input name="BIOSEQ_FORMAT_TYPE" value="ASN.1" size="3" id="bioseqFormat" type="text" class="hidden dispType" />
|
144
|
+
<input name="PSSM_SC_FORMAT_TYPE" value="ASN.1" size="3" id="pssmScFormat" type="text" class="hidden dispType" />
|
145
|
+
<span id="advView" class="">
|
146
|
+
<span class=""><input name="OLD_VIEW" id="OLD_VIEW" type="checkbox" class="cb reset" defVal="checked" />
|
147
|
+
<label for="OLD_VIEW">Old View</label></span>
|
148
|
+
</span>
|
149
|
+
<a class="resetAll" id="resetAll" >Reset form to defaults</a>
|
150
|
+
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Alignments object formatting help" id="formatHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
|
151
|
+
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
|
152
|
+
<div class="ui-helper-reset" aria-live="assertive" >
|
153
|
+
<p class="helpbox ui-ncbitoggler-slave" id="hlp1">
|
154
|
+
These options control formatting of alignments in results pages. The
|
155
|
+
default is HTML, but other formats (including plain text) are available.
|
156
|
+
PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST.
|
157
|
+
The Advanced view option allows the database descriptions to be sorted by various indices in a table.
|
158
|
+
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#format_object" target="helpWin" title="Additional alignments object formatting help">more...</a>
|
159
|
+
</p>
|
160
|
+
</div><!-- ARIA -->
|
161
|
+
</div>
|
162
|
+
</td>
|
163
|
+
</tr>
|
164
|
+
|
165
|
+
<tr class="odd paramSet">
|
166
|
+
<td class="hd"><label for="ALIGNMENT_VIEW">Alignment View</label></td>
|
167
|
+
<td>
|
168
|
+
<div class="fi">
|
169
|
+
<select name="ALIGNMENT_VIEW" id="ALIGNMENT_VIEW" defVal="Pairwise" class="reset">
|
170
|
+
<option value="Pairwise" >Pairwise</option>
|
171
|
+
<option value="PairwiseWithIdentities" >Pairwise with dots for identities</option>
|
172
|
+
<option value="QueryAnchored" >Query-anchored with dots for identities</option>
|
173
|
+
<option value="QueryAnchoredNoIdentities" >Query-anchored with letters for identities</option>
|
174
|
+
<option value="FlatQueryAnchored" >Flat query-anchored with dots for identities</option>
|
175
|
+
<option value="FlatQueryAnchoredNoIdentities" >Flat query-anchored with letters for identities</option>
|
176
|
+
<option value="Tabular" >Hit Table</option>
|
177
|
+
</select>
|
178
|
+
|
179
|
+
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Alignments view options help" id="alnViewHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
|
180
|
+
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
|
181
|
+
<div class="ui-helper-reset" aria-live="assertive" >
|
182
|
+
<p class="helpbox ui-ncbitoggler-slave" id="hlp2">
|
183
|
+
Choose how to view alignments.
|
184
|
+
The default "pairwise" view shows how each subject sequence aligns
|
185
|
+
individually to the query sequence. The "query-anchored" view shows how
|
186
|
+
all subject sequences align to the query sequence. For each view type,
|
187
|
+
you can choose to show "identities" (matching residues) as letters or
|
188
|
+
dots.
|
189
|
+
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#alignment_view" target="helpWin" title="Additional alignments view options help">more...</a>
|
190
|
+
</p>
|
191
|
+
</div><!-- ARIA -->
|
192
|
+
</div>
|
193
|
+
</td>
|
194
|
+
</tr>
|
195
|
+
|
196
|
+
<tr class="paramSet">
|
197
|
+
<td class="hd"><label>Display</label></td>
|
198
|
+
<td class="cb">
|
199
|
+
<div class="fi">
|
200
|
+
<input name="SHOW_OVERVIEW" id="SHOW_OVERVIEW" type="checkbox" class="cb reset" defVal="checked" checked="checked" />
|
201
|
+
<label class="rb" for="SHOW_OVERVIEW">Graphical Overview</label>
|
202
|
+
|
203
|
+
<span id="shl" >
|
204
|
+
<input name="SHOW_LINKOUT" id="SHOW_LINKOUT" type="checkbox" class="cb reset" defVal="checked" checked="checked" />
|
205
|
+
<label class="rb" for="SHOW_LINKOUT">Linkout</label>
|
206
|
+
</span>
|
207
|
+
<span id="gts" >
|
208
|
+
<input name="GET_SEQUENCE" id="GET_SEQUENCE" type="checkbox" class="cb reset" defVal="checked" checked="checked" />
|
209
|
+
<label class="rb" for="GET_SEQUENCE">Sequence Retrieval</label>
|
210
|
+
</span>
|
211
|
+
|
212
|
+
<input name="NCBI_GI" id="NCBI_GI" type="checkbox" class="cb reset" defVal="unchecked" checked="checked" />
|
213
|
+
<label class="rb" for="NCBI_GI">NCBI-gi</label>
|
214
|
+
<span id="scf" >
|
215
|
+
<input name="SHOW_CDS_FEATURE" id="SHOW_CDS_FEATURE" type="checkbox" class="cb reset blastn" defVal="unchecked" />
|
216
|
+
<label for="SHOW_CDS_FEATURE" class="blastn">CDS feature</label>
|
217
|
+
</span>
|
218
|
+
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Alignments display options help" id="displayHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
|
219
|
+
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
|
220
|
+
<div class="ui-helper-reset" aria-live="assertive" >
|
221
|
+
<ul class="helpbox ui-ncbitoggler-slave" id="hlp3">
|
222
|
+
<li>Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to query.
|
223
|
+
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_overview" target="helpWin" title="Graphical Overview help">more...</a>
|
224
|
+
</li>
|
225
|
+
<li>Database LinkOuts: Show links from matching sequences to entries in specialized NCBI databases.
|
226
|
+
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_linkout" title="LinkOut help" target="helpWin" >more...</a>
|
227
|
+
</li>
|
228
|
+
<li>Sequence Retrieval: Show buttons to download matching sequences.
|
229
|
+
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#get_sequence" title="Sequence Retrieval help" target="helpWin" >more...</a>
|
230
|
+
</li>
|
231
|
+
<li>NCBI-gi: Show NCBI gi identifiers.
|
232
|
+
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#ncbi_gi" title="NCBI-gi help" target="helpWin" >more...</a>
|
233
|
+
</li>
|
234
|
+
<li>CDS feature: Show annotated coding region and translation.
|
235
|
+
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#show_cds_feature" title="CDS feature help" target="helpWin" >more...</a>
|
236
|
+
</li></ul>
|
237
|
+
</div><!-- ARIA -->
|
238
|
+
</div>
|
239
|
+
</td>
|
240
|
+
</tr>
|
241
|
+
|
242
|
+
|
243
|
+
<tr class="paramSet odd xgl">
|
244
|
+
<td class="hd"><label>Masking</label></td>
|
245
|
+
<td>
|
246
|
+
<div class="fi">
|
247
|
+
<label for="MASK_CHAR"> Character: </label>
|
248
|
+
<select name="MASK_CHAR" id="MASK_CHAR" class="reset" defVal="2">
|
249
|
+
<option value="0" >X for protein, n for nucleotide</option>
|
250
|
+
<option value="2" selected="selected" >Lower Case</option>
|
251
|
+
</select>
|
252
|
+
<label for="MASK_COLOR"> Color:</label>
|
253
|
+
<select name="MASK_COLOR" id="MASK_COLOR" class="reset" defVal="1">
|
254
|
+
<option value="0" >Black
|
255
|
+
</option>
|
256
|
+
|
257
|
+
<option value="1" selected="selected" >Grey
|
258
|
+
</option>
|
259
|
+
|
260
|
+
<option value="2" >Red
|
261
|
+
</option>
|
262
|
+
|
263
|
+
</select>
|
264
|
+
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Alignments masking help" id="maskingHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
|
265
|
+
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
|
266
|
+
<div class="ui-helper-reset" aria-live="assertive" >
|
267
|
+
<ul class="helpbox ui-ncbitoggler-slave" id="hlp4">
|
268
|
+
<li>Masking Character: Display masked (filtered) sequence regions as lower-case or as specific letters (N for nucleotide, P for protein).
|
269
|
+
</li>
|
270
|
+
<li>Masking Color: Display masked sequence regions in the given color.</li>
|
271
|
+
</ul>
|
272
|
+
</div><!-- ARIA -->
|
273
|
+
</div>
|
274
|
+
</td>
|
275
|
+
</tr>
|
276
|
+
|
277
|
+
|
278
|
+
<tr class="paramSet xgl">
|
279
|
+
<td class="hd"><label>Limit results</label></td>
|
280
|
+
<td>
|
281
|
+
<div class="fi">
|
282
|
+
<label for="FRM_DESCRIPTIONS">Descriptions:</label>
|
283
|
+
<select name="DESCRIPTIONS" id="FRM_DESCRIPTIONS" class="reset" defVal="100">
|
284
|
+
<option value="0" >0</option>
|
285
|
+
<option value="10" >10</option>
|
286
|
+
<option value="50" >50</option>
|
287
|
+
<option value="100" selected="selected" >100</option>
|
288
|
+
<option value="250" >250</option>
|
289
|
+
<option value="500" >500</option>
|
290
|
+
<option value="1000" >1000</option>
|
291
|
+
<option value="5000" >5000</option>
|
292
|
+
<option value="10000" >10000</option>
|
293
|
+
<option value="20000" >20000</option>
|
294
|
+
</select>
|
295
|
+
|
296
|
+
<label for="FRM_NUM_OVERVIEW">Graphical overview:</label>
|
297
|
+
<select name="NUM_OVERVIEW" id="FRM_NUM_OVERVIEW" class="reset" defVal="100">
|
298
|
+
<option value="0" >0</option>
|
299
|
+
<option value="10" >10</option>
|
300
|
+
<option value="50" >50</option>
|
301
|
+
<option value="100" selected="selected" >100</option>
|
302
|
+
<option value="250" >250</option>
|
303
|
+
<option value="500" >500</option>
|
304
|
+
<option value="1000" >1000</option>
|
305
|
+
</select>
|
306
|
+
<span id="frmAln">
|
307
|
+
<label for="FRM_ALIGNMENTS">Alignments:</label>
|
308
|
+
<select name="ALIGNMENTS" id="FRM_ALIGNMENTS" class="reset" defVal="100">
|
309
|
+
<option value="0" >0</option>
|
310
|
+
<option value="10" >10</option>
|
311
|
+
<option value="50" >50</option>
|
312
|
+
<option value="100" selected="selected" >100</option>
|
313
|
+
<option value="250" >250</option>
|
314
|
+
<option value="500" >500</option>
|
315
|
+
<option value="1000" >1000</option>
|
316
|
+
<option value="5000" >5000</option>
|
317
|
+
<option value="10000" >10000</option>
|
318
|
+
<option value="20000" >20000</option>
|
319
|
+
</select>
|
320
|
+
</span>
|
321
|
+
<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>
|
322
|
+
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
|
323
|
+
<div class="ui-helper-reset" aria-live="assertive" >
|
324
|
+
<ul class="helpbox ui-ncbitoggler-slave" id="hlp5">
|
325
|
+
<li>Descriptions: Show short descriptions for up to the given number of sequences.</li>
|
326
|
+
<li>Alignments: Show alignments for up to the given number of sequences, in order of statistical significance.</li>
|
327
|
+
</ul>
|
328
|
+
</div><!-- ARIA -->
|
329
|
+
</div>
|
330
|
+
</td>
|
331
|
+
</tr>
|
332
|
+
|
333
|
+
<tr class="paramSet odd xgl">
|
334
|
+
<td class="hd"></td>
|
335
|
+
<td>
|
336
|
+
<div class="">
|
337
|
+
<label for="qorganism">Organism</label>
|
338
|
+
<span class="instr">Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown.</span><br>
|
339
|
+
<input name="FORMAT_ORGANISM" size="55" type="text" id="qorganism" value="" data-jigconfig="dictionary:'taxids_sg'" autocomplete="off" class="jig-ncbiautocomplete reset">
|
340
|
+
<input type="checkbox" name="FORMAT_ORG_EXCLUDE" class="oExclR cb" id="orgExcl"/>
|
341
|
+
<input type="hidden" value = "1" name="FORMAT_NUM_ORG" id="numOrg" />
|
342
|
+
<label for="orgExcl" class="right">Exclude</label>
|
343
|
+
<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>
|
344
|
+
<div id="orgs">
|
345
|
+
|
346
|
+
</div>
|
347
|
+
<div class="fi">
|
348
|
+
<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>
|
349
|
+
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
|
350
|
+
<div class="ui-helper-reset" aria-live="assertive" >
|
351
|
+
<p class="helpbox ui-ncbitoggler-slave" id="hlp6">
|
352
|
+
Show only sequences from the given organism.
|
353
|
+
</p>
|
354
|
+
</div><!-- ARIA -->
|
355
|
+
</div>
|
356
|
+
</div>
|
357
|
+
</td>
|
358
|
+
</tr>
|
359
|
+
|
360
|
+
<tr class="paramSet xgl">
|
361
|
+
<td class="hd"></td>
|
362
|
+
<td>
|
363
|
+
<div class="fi">
|
364
|
+
<label for="FORMAT_EQ_TEXT">Entrez query:</label>
|
365
|
+
<input name="FORMAT_EQ_TEXT" id="FORMAT_EQ_TEXT" size="60" type="text" value="" class="reset" />
|
366
|
+
<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>
|
367
|
+
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
|
368
|
+
<div class="ui-helper-reset" aria-live="assertive" >
|
369
|
+
<p class="helpbox ui-ncbitoggler-slave" id="hlp7">
|
370
|
+
Show only those sequences that match the given Entrez query.
|
371
|
+
<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>
|
372
|
+
</p>
|
373
|
+
</div><!-- ARIA -->
|
374
|
+
</div>
|
375
|
+
</td>
|
376
|
+
</tr>
|
377
|
+
|
378
|
+
|
379
|
+
<tr class="paramSet odd xgl">
|
380
|
+
<td class="hd"></td>
|
381
|
+
<td>
|
382
|
+
<div class="fi">
|
383
|
+
<label for="EXPECT_LOW">Expect Min:</label> <input name="EXPECT_LOW" id="EXPECT_LOW" size="10" type="text" value="" class="reset"/>
|
384
|
+
<label for="EXPECT_HIGH">Expect Max:</label> <input name="EXPECT_HIGH" id="EXPECT_HIGH" size="10" type="text" value="" class="reset" />
|
385
|
+
<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>
|
386
|
+
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
|
387
|
+
<div class="ui-helper-reset" aria-live="assertive" >
|
388
|
+
<p class="helpbox ui-ncbitoggler-slave" id="hlp8">
|
389
|
+
Show only sequences with expect values in the given range.
|
390
|
+
<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>
|
391
|
+
</p>
|
392
|
+
</div><!-- ARIA -->
|
393
|
+
</div>
|
394
|
+
</td>
|
395
|
+
</tr>
|
396
|
+
<tr class="paramSet xgl">
|
397
|
+
<td class="hd"></td>
|
398
|
+
<td>
|
399
|
+
<div class="fi">
|
400
|
+
<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"/>
|
401
|
+
<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" />
|
402
|
+
<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>
|
403
|
+
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
|
404
|
+
<div class="ui-helper-reset" aria-live="assertive" >
|
405
|
+
<p class="helpbox ui-ncbitoggler-slave" id="hlp10">
|
406
|
+
Show only sequences with percent identity values in the given range.
|
407
|
+
</p>
|
408
|
+
</div><!-- ARIA -->
|
409
|
+
</div>
|
410
|
+
</td>
|
411
|
+
</tr>
|
412
|
+
<tr class="psiBlast odd paramSet xgl">
|
413
|
+
<td class="hd"><label>Format for</label></td>
|
414
|
+
<td>
|
415
|
+
<div class="fi">
|
416
|
+
<input name="RUN_PSIBLAST_FORM" id="RUN_PSIBLAST" type="checkbox" class="cb psiBlast" />
|
417
|
+
<label class="rb psiBlast" for="RUN_PSIBLAST">PSI-BLAST</label>
|
418
|
+
<label for="I_THRESH">with inclusion threshold:</label>
|
419
|
+
<input name="I_THRESH" id="I_THRESH" size="10" type="text" value="" defVal="0.005" />
|
420
|
+
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="PSI BLAST formatting help" id="psiHelp" href="#"><span class="ui-ncbitoggler-master-text"><span>[?]</span></span>
|
421
|
+
<span class="ui-icon ui-icon-triangle-1-e"></span></a>
|
422
|
+
<div class="ui-helper-reset" aria-live="assertive" >
|
423
|
+
<ul class="helpbox ui-ncbitoggler-slave" id="hlp9">
|
424
|
+
<li>Format for PSI-BLAST: The Position-Specific Iterated BLAST (PSI-BLAST) program performs iterative searches with a protein query,
|
425
|
+
in which sequences found in one round of search are used to build a custom score model for the next round.
|
426
|
+
<a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#psiblast" target="helpWin" title="Additional PSI BLAST formatting help">more...</a>
|
427
|
+
</li>
|
428
|
+
<li>Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used
|
429
|
+
by PSI-BLAST to create the PSSM on the next iteration.</li>
|
430
|
+
</ul>
|
431
|
+
</div><!-- ARIA -->
|
432
|
+
</div>
|
433
|
+
</td>
|
434
|
+
</tr>
|
435
|
+
</table>
|
436
|
+
</dd>
|
437
|
+
</dl>
|
438
|
+
|
439
|
+
<input name="RID" value="BUCSAKD101R" type="hidden" />
|
440
|
+
<input name="CDD_RID" value="" type="hidden" />
|
441
|
+
<input name="CDD_SEARCH_STATE" type="hidden" value="" />
|
442
|
+
|
443
|
+
<input name="STEP_NUMBER" value="" id="stepNumber" type="hidden" />
|
444
|
+
<input name="CMD" value="Get" type="hidden" />
|
445
|
+
<input name="FORMAT_EQ_OP" value="AND" type="hidden" />
|
446
|
+
<input name="RESULTS_PAGE_TARGET" type="hidden" id="resPageTarget" value="Blast_Results_for_2041855348" />
|
447
|
+
<input name="QUERY_INFO" type="hidden" value="gi|555 (624 letters)" />
|
448
|
+
|
449
|
+
<input name="ENTREZ_QUERY" type="hidden" value="" />
|
450
|
+
<input name="QUERY_INDEX" type="hidden" value="0"/>
|
451
|
+
<input name="NUM_QUERIES" type="hidden" value="1"/>
|
452
|
+
<input name="CONFIG_DESCR" type="hidden" value="2,3,4,5,6,7,8" />
|
453
|
+
|
454
|
+
<!-- Those params are set in the template (blastn.dat, blastp.dat etc. -->
|
455
|
+
<input name="BLAST_PROGRAMS" type="hidden" value="blastn"/>
|
456
|
+
<input name="PAGE" type="hidden" value="Nucleotides"/>
|
457
|
+
<input name="PROGRAM" type="hidden" value="blastn"/>
|
458
|
+
<input name="MEGABLAST" type="hidden" value="" />
|
459
|
+
<input name="RUN_PSIBLAST" type="hidden" value="" />
|
460
|
+
<input name="BLAST_SPEC" id="blastSpec" type="hidden" value=""/>
|
461
|
+
|
462
|
+
|
463
|
+
<input name="QUERY" type="hidden" value=""/>
|
464
|
+
<input name="JOB_TITLE" type="hidden" value="gi|555 (624 letters)"/>
|
465
|
+
<input name="QUERY_TO" type="hidden" value=""/>
|
466
|
+
<input name="QUERY_FROM" type="hidden" value=""/>
|
467
|
+
<input name="EQ_TEXT" type="hidden" value=""/>
|
468
|
+
<input name="ORGN" type="hidden" value=""/>
|
469
|
+
<input name="EQ_MENU" type="hidden" value=""/>
|
470
|
+
<input name="ORG_EXCLUDE" type="hidden" value=""/>
|
471
|
+
<input name="PHI_PATTERN" type="hidden" value=""/>
|
472
|
+
<input name="EXPECT" type="hidden" value="10"/>
|
473
|
+
<input name="DATABASE" type="hidden" value="nr"/>
|
474
|
+
<input name="DB_GROUP" type="hidden" value=""/>
|
475
|
+
<input name="SUBGROUP_NAME" type="hidden" value=""/>
|
476
|
+
|
477
|
+
<input name="GENETIC_CODE" type="hidden" value=""/>
|
478
|
+
<input name="WORD_SIZE" type="hidden" value=""/>
|
479
|
+
<input name="MATCH_SCORES" type="hidden" value=""/>
|
480
|
+
<input name="MATRIX_NAME" type="hidden" value=""/>
|
481
|
+
<input name="GAPCOSTS" type="hidden" value=""/>
|
482
|
+
<input name="MAX_NUM_SEQ" id="maxNumSeq" type="hidden" value=""/>
|
483
|
+
|
484
|
+
<input name="COMPOSITION_BASED_STATISTICS" type="hidden" value=""/>
|
485
|
+
<input name="NEWWIN" type="hidden" value=""/>
|
486
|
+
<input name="SHORT_QUERY_ADJUST" type="hidden" value=""/>
|
487
|
+
<input name="FILTER" type="hidden" value="L ;"/>
|
488
|
+
<input name="REPEATS" type="hidden" value=""/>
|
489
|
+
<input name="ID_FOR_PSSM" type="hidden" value=""/>
|
490
|
+
<input name="EXCLUDE_MODELS" type="hidden" value=""/>
|
491
|
+
<input name="EXCLUDE_SEQ_UNCULT" type="hidden" value=""/>
|
492
|
+
<input name="NUM_ORG" type="hidden" value = "1" />
|
493
|
+
|
494
|
+
<!-- PSSM -->
|
495
|
+
<input name="LCASE_MASK" type="hidden" value=""/>
|
496
|
+
<input name="TEMPLATE_TYPE" type="hidden" value=""/>
|
497
|
+
<input name="TEMPLATE_LENGTH" type="hidden" value=""/>
|
498
|
+
<input name="I_THRESH" type="hidden" value=""/>
|
499
|
+
<input name="PSI_PSEUDOCOUNT" type="hidden" value=""/>
|
500
|
+
<input name="DI_THRESH" type="hidden" id="diThresh" value=""/>
|
501
|
+
<input name="HSP_RANGE_MAX" type="hidden" value=""/>
|
502
|
+
|
503
|
+
|
504
|
+
|
505
|
+
<input name="ADJUSTED_FOR_SHORT_QUERY" type="hidden" value=""/>
|
506
|
+
<input name="MIXED_QUERIES" type="hidden" value=""/>
|
507
|
+
<input name="MIXED_DATABASE" id="mixedDb" type="hidden" value=""/>
|
508
|
+
<input name="BUILD_NAME" type="hidden" value=""/>
|
509
|
+
<input name="ORG_DBS" type="hidden" value=""/>
|
510
|
+
|
511
|
+
<!--QBlastInfoBegin
|
512
|
+
RID = BUCSAKD101R
|
513
|
+
RTOE = 17
|
514
|
+
QBlastInfoEnd
|
515
|
+
-->
|
516
|
+
</form>
|
517
|
+
|
518
|
+
</div><!-- /#content -->
|
519
|
+
|
520
|
+
</div><!-- /#content-wrap -->
|
521
|
+
|
522
|
+
|
523
|
+
<div id="footer">
|
524
|
+
<div id="rgs">BLAST is a registered trademark of the National Library of Medicine.</div>
|
525
|
+
<p id="orgns">
|
526
|
+
<a href="http://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information">NCBI</a> |
|
527
|
+
<a href="http://www.nlm.nih.gov/" title="National Library of Medicine">NLM</a> |
|
528
|
+
<a href="http://www.nih.gov/" title="National Institutes of Health">NIH</a> |
|
529
|
+
<a href="http://www.hhs.gov/" title="US Department of Health and Human Services">DHHS</a>
|
530
|
+
</p>
|
531
|
+
|
532
|
+
<p>
|
533
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html'
|
534
|
+
title='NCBI intellectual property statement'>Copyright</a> |
|
535
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/disclaimer.html#disclaimer'
|
536
|
+
title='About liability, endorsements, external links, pop-up advertisements'>Disclaimer</a> |
|
537
|
+
<a href='http://www.nlm.nih.gov/privacy.html'
|
538
|
+
title='NLM privacy policy'>Privacy</a> |
|
539
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/accessibility.html'
|
540
|
+
title='About using NCBI resources with assistive technology'>Accessibility</a> |
|
541
|
+
<a href='http://www.ncbi.nlm.nih.gov/About/glance/contact_info.html'
|
542
|
+
title='How to get help, submit data, or provide feedback'>Contact</a> |
|
543
|
+
<a href='mailto:blast-help@ncbi.nlm.nih.gov'
|
544
|
+
title='How to get help, submit data, or provide feedback'>Send feedback</a>
|
545
|
+
</p>
|
546
|
+
</div>
|
547
|
+
</div><!--/#wrap-->
|
548
|
+
|
549
|
+
<script type="text/javascript" src="http://blast.ncbi.nlm.nih.gov/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js"></script>
|
550
|
+
</body>
|
551
|
+
|
552
|
+
</html>
|
553
|
+
|