1141 lines
76 KiB
HTML
1141 lines
76 KiB
HTML
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<meta name="jig" content="ncbitoggler ncbiautocomplete"/>
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<meta name="ncbi_app" content="igblast" />
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<title>IgBlast tool</title>
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<nav class="ncbi-topnav" id="navcontent">
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<div class="usa-grid">
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<a class="lf" href="index.cgi">IGBLAST</a>
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<span id="brc">A tool for immunoglobulin (IG) and T cell receptor (TR) V domain sequences</span>
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<span class="rf"></span>
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</div>
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</nav>
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<span class="pagelinks">
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<label>Documentation:</label>
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<a href="intro.html" target="helpWin">Introduction</a>
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<a href="faq.html#ref" target="helpWin">Reference</a>
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<a href="faq.html" target="helpWin">FAQs</a>
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<a href="https://ncbi.github.io/igblast/" target="helpWin">Stand-alone IgBLAST</a>
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<a href="showGermline.cgi" target="helpWin">Ig Germline Genes</a>
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<a href="resources.html" target="helpWin">Other Resources</a>
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</span>
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<div id="content">
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<!-- Do errors this way -->
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<ul class="msg "><li class=""><p class=""></p></li></ul>
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<div class="bc-tabs">
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<ul>
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<li class="tab-current"><input type="button" class="usa-button progLinks" id="IGTab" proglink="igblast.cgi?CMD=Web&SEARCH_TYPE=IG&LINK_LOC=igtab" title="Search a nucleotide databases using a nucleotide query" value="Analyze immunoglobulin (Ig) sequences"></li>
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<li><input type="button" class="usa-button progLinks" id="TCRTab" proglink="igblast.cgi?CMD=Web&SEARCH_TYPE=TCR&LINK_LOC=igtab" title="Search a protein databases using a protein query" value="Analyze T cell receptor (TR) sequences"></li>
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</ul>
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</div>
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<form name="searchForm" action="./igblast.cgi" enctype="multipart/form-data" method="post" class="f-wrap-1 " id="searchForm">
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<div class="pagelinks" id="pgl">
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<span class="lnk">
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<a href="retrieve.html" id="retrieve">Retrieve recent results</a>
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</span>
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<button class="usa-button-secondary" id="resetlink" resetform="searchForm">Reset page</button>
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<button class="usa-button-secondary" name="getURL" id="getURL">Save search parameters</button>
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</div>
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<div id="query" class="section">
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<fieldset>
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<legend> Enter Query Sequence</legend>
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<div class="formblock " id="qseq">
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<label for="queryseq">Enter sequence(s)</label>
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<a class="helplink jig-ncbitoggler ui-ncbitoggler" data-ncbitoggler-toggles="qhelp" title="Enter query sequnce help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
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<button class="usa-button-secondary clearlink" fieldtoclear="queryseq" id="clearseq">Clear</button>
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<div class="ui-helper-reset" aria-live="assertive" >
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<div id="qhelp" class="helpbox ui-ncbitoggler-slave">
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<p>Sequence can be in form of raw sequence, accession # or gi (example accession Y14934). You may opt to
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||
include a definition line starting with ">" at the top in conforming to FASTA format.
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||
You can also load your sequences contained in a local file (make sure it is a plain text file).
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||
If the sequence is already in GenBank, you can just enter its accession or gi #.
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||
</p>
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||
<p>Multiple query sequences may be submitted. Each sequence must have a unique identifier and we suggest
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||
that you do not use white spaces in the identifier as any characters after the white spaces will be excluded.
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||
</p>
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||
</div>
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||
</div><!-- ARIA -->
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||
<textarea id="queryseq" class="reset" rows="5" cols="80" name="queryseq" ></textarea>
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||
<br />
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||
<label for="upl" class="m" >Or, upload local sequence file</label>
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||
<div class="input ">
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||
<input type="file" id="upl" name="queryfile" />
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||
</div>
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||
</div>
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||
</fieldset>
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||
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||
<fieldset class=" section">
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||
<legend> Germline gene databases</legend>
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||
<label class="m" for="organism">Organism for query sequence</label>
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||
<div class="input ">
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||
<select name="organism" id="organism" class="reset" >
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||
<a href="./help.html#Origin" target="info">Organism for query sequence</a>
|
||
<option selected="selected" value ="human" >Human</option>
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||
<option value ="mouse" >Mouse</option>
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||
<option value ="rat" >Rat</option>
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||
<option value ="rabbit" >Rabbit</option>
|
||
<option value ="rhesus_monkey" >Rhesus monkey</option>
|
||
</select>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Organism help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
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<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
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||
Specify the organism which the query sequence comes from. This allows the program to properly report the
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V domain delineation, the V-J frame status (i.e, in-frame, out-of-frame, etc) and the translation of the query nucleotide sequence.
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
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||
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||
<label class="m" for="germline_db_V">Germline V gene Database</label>
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||
<div class="input vgene">
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||
<div>
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||
<span class="nonDefPar">♦<span class="acPromt">Germline V gene Database non-default value</span></span>
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||
<select name="germline_db_V" id="germline_db_V" class="reset checkDef par" customFile="cst_db_V" defVal="" >
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||
<option selected="selected" class="Deflt" value="IG_DB/imgt.Homo_sapiens.V.f.orf.p" >IMGT human V genes (F+ORF+in-frame P)</option>
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||
<option value="IG_DB/airr_c_human_ig.V" >AIRR-C human germline V gene set</option>
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||
<option value="IG_DB/human_gl_V" >NCBI human V genes</option>
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||
<option value="IG_DB/imgt.Homo_sapiens.V.f.orf" >IMGT human V genes (F+ORF)</option>
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||
<option value="IG_DB/imgt.Homo_sapiens.V.p" >IMGT human V genes (In-frame P)</option>
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||
<option value="IG_DB/imgt.Homo_sapiens.V.f.orf.p.include_orp" >IMGT human V genes (F+ORF+in-frame P) including orphons</option>
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||
<option value="IG_DB/imgt.Homo_sapiens.V.f.orf.include_orp" >IMGT human V genes (F+ORF) including orphons</option>
|
||
<option value="IG_DB/imgt.Homo_sapiens.V.p.include_orp" >IMGT human V genes (In-frame P) including orphons</option>
|
||
<option value="IG_DB/human_gl_V.old" >NCBI human V genes (old)</option>
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||
<option value="custom" >Custom</option>
|
||
</select>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Germline V gene Database help" data-ncbitoggler-toggles="gdvhelp" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
</div>
|
||
<div id="cst_db_V" class="hidden">Upload file<input name="custom_db_V" type="file"></div>
|
||
<div id="gdvhelp" class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
<p>
|
||
All IMGT germline databases are from <a href="http://www.imgt.org/vquest/refseqh.html">IMGT/V-QUEST reference directory sets</a>.
|
||
Sequences from several different categories are available including functional genes (F),
|
||
open reading frame genes (ORF), pseudogenes whose protein translation frames are intact (in-frame P)
|
||
and orphon genes that are outside of normal immunoglobulin or T cell receptor gene loci.
|
||
</p>
|
||
|
||
<p class="hp human vgene">
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||
AIRR-C V genes are from <a href="https://ogrdb.airr-community.org/">AIRR community</a>.
|
||
</p>
|
||
|
||
<p class="hp human vgene">
|
||
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||
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||
NCBI human V genes:
|
||
This database consists of the "IMGT human V genes (F+ORF+in-frame P) including orphons" database plus
|
||
a few pseudogenes that IMGT database did not include. It contains the same human sequences as the "Ig germline V genes" database for the previous version of IgBLAST.
|
||
</p>
|
||
|
||
<p class="hp human vgene">
|
||
NCBI human V genes (old):
|
||
This is our earliest version of human Ig germline V genes database before addition of the human germline sequences from IMGT database.
|
||
It is the same as "Ig germline V genes (old)" database for the previous version of IgBLAST.
|
||
</p>
|
||
|
||
<p class="hp mouse">
|
||
AIRR-C V genes are from <a href="https://ogrdb.airr-community.org/">AIRR community</a>.
|
||
</p>
|
||
</p>
|
||
NCBI mouse V genes, NCBI mouse D genes and NCBI mouse J genes:
|
||
These are mouse germline sequences independently collected by NCBI.
|
||
</p>
|
||
|
||
<p class="hp rhesus_monkey">
|
||
Rhesus monkey germline V, D, J genes are Macaca Mulatta germline sequence collections from <a href="http://kimdb.gkhlab.se/">KIMDB</a>.
|
||
|
||
</p>
|
||
<p>
|
||
See <a href="https://www.ncbi.nlm.nih.gov/igblast/showGermline.cgi">NCBI germline genes</a> for details on NCBI germline gene collections.
|
||
</p>
|
||
<p>
|
||
Custom:
|
||
You can search your own database. Your database should contain sequences in FASTA format.
|
||
</p>
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label class="m blastp" for="germline_db_D">Germline D gene Database</label>
|
||
<div class="input blastp">
|
||
<div>
|
||
<span class="nonDefPar">♦<span class="acPromt">Germline D gene Database non-default value</span></span>
|
||
<select name="germline_db_D" id="germline_db_D" class="reset checkDef par" customFile="cst_db_D" defVal="" >
|
||
<option selected="selected" class="Deflt" value="IG_DB/imgt.Homo_sapiens.D.f.orf" >IMGT human D genes (F+ORF)</option>
|
||
<option value="IG_DB/airr_c_human_igh.D" >AIRR-C human germline D gene set</option>
|
||
<option value="IG_DB/imgt.Homo_sapiens.D.f.orf.include_orp" >IMGT human D genes (F+ORF) including orphons</option>
|
||
<option value="IG_DB/human_gl_D.old" >NCBI human D genes (old)</option>
|
||
<option value="custom" >Custom</option>
|
||
</select>
|
||
|
||
</div>
|
||
<div id="cst_db_D" class="hidden">Upload file<input name="custom_db_D" type="file"></div>
|
||
|
||
</div>
|
||
|
||
<label class="m blastp" for="germline_db_J">Germline J gene Database</label>
|
||
<div class="input jgene blastp">
|
||
<div>
|
||
<span class="nonDefPar">♦<span class="acPromt">Germline J gene Database non-default value</span></span>
|
||
<select name="germline_db_J" id="germline_db_J" class="reset checkDef par" customFile="cst_db_J" defVal="" >
|
||
<option selected="selected" class="Deflt" value="IG_DB/imgt.Homo_sapiens.J.f.orf" >IMGT human J genes (F+ORF)</option>
|
||
<option value="IG_DB/airr_c_human_ig.J" >AIRR-C human germline J gene set</option>
|
||
<option value="IG_DB/human_gl_J.old" >NCBI human J genes (old)</option>
|
||
<option value="custom" >Custom</option>
|
||
</select>
|
||
|
||
</div>
|
||
<div id="cst_db_J" class="hidden">Upload file<input name="custom_db_J" type="file"></div>
|
||
|
||
</div>
|
||
|
||
|
||
<div class="germline_db_C">
|
||
<label class="m blastp germline_db_C" for="germline_db_C">Germline C gene Database   </label>
|
||
<div class="input blastp">
|
||
<div>
|
||
<span class="nonDefPar">♦<span class="acPromt">Germline C gene Database non-default value</span></span>
|
||
<select name="germline_db_C" id="germline_db_C" class="reset checkDef par" customFile="cst_db_C" defVal="" >
|
||
|
||
</select>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Germline C gene Database help" data-ncbitoggler-toggles="gdchelp" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
</div>
|
||
<div id="cst_db_C" class="hidden">Upload file<input name="custom_db_C" type="file"></div> <div id="gdchelp" class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
<p>
|
||
The C gene match is intended for rearranged Ig sequences which means your Ig sequence needs to have the V(D)J part preceding the C region.
|
||
</p>
|
||
<p>
|
||
NCBI human C gene database:
|
||
</p>
|
||
<p>
|
||
This is the Constant region genes annotated on NCBI reference genome. Since this is from the reference genome only, additional alleles are not included. Note that, to be consistent with IMGT's reference C gene sequence, an extra base (from the J gene end) is added to the start of the C gene sequence to maintain the completeness of the first codon for C gene, and as a result, the IgBLAST result typically shows a one base overlap between J and C genes.
|
||
|
||
</p>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
</fieldset>
|
||
<div>
|
||
|
||
<fieldset class="section">
|
||
<legend>Search Parameters</legend>
|
||
|
||
<label class="m" for="program">Program</label>
|
||
<div class="input">
|
||
<span class="nonDefPar">♦<span class="acPromt">Program non-default value</span></span>
|
||
<select name="program" id="program" class="reset checkDef par" defVal="blastn" >
|
||
<option selected="selected" value="blastn" >blastn</option>
|
||
<option value="blastp" >blastp</option>
|
||
</select>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Program help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
Choose blastp for protein sequences and blastn for nucleotide sequences.
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label class="m blastp" for="mismatch_penalty">V gene mismatch penalty</label>
|
||
<div class="input blastp">
|
||
<span class="nonDefPar">♦<span class="acPromt">V gene mismatch penalty non-default value</span></span>
|
||
<select name="mismatch_penalty" id="mismatch_penalty" class="reset checkDef par" defVal="" >
|
||
<option selected="selected" value="-1" >-1</option>
|
||
<option value="-2" >-2</option>
|
||
<option value="-3" >-3</option>
|
||
</select>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Mismatch penalty for V gene help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
A higher mismatch penalty (for example, -3) favors detecting V gene matches with higher similarity to the query sequence but such matched regions are not necessarily long. On the other hand, a lower mismatch penalty (for example, -1) favors detecting longer V gene matches that do not necessarily have a high similarity to the query sequence. In general, a higher penalty works better if your sequence has few or no somatic mutations. But if your sequence has significant mutations (>5%),then a lower penalty should be chosen if you want to accommodate the low similarity introduced by mutations.
|
||
<br><br>
|
||
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
|
||
<label class="m blastp" for="min_D_match">Min D gene nucleotide matches</label>
|
||
<div class="input blastp">
|
||
<span class="nonDefPar">♦<span class="acPromt">Min D gene nucleotide matches non-default value</span></span>
|
||
<select name="min_D_match" id="min_D_match" class="reset checkDef par" defVal="" >
|
||
<option selected="selected" value="5" >5</option>
|
||
<option value="6" >6</option>
|
||
<option value="7" > 7</option>
|
||
<option value="8" >8</option>
|
||
<option value="9" >9</option>
|
||
<option value="10" >10</option>
|
||
<option value="11" >11</option>
|
||
<option value="12" >12</option>
|
||
<option value="13" >13</option>
|
||
<option value="14" >14</option>
|
||
<option value="15" >15</option>
|
||
</select>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Min consecutive nucleotide matches for D gene help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
This controls the threshold for D gene detection. You can set the minimal number of required consecutive nucleotide matches
|
||
between the query sequence and the D genes based on your own criteria. Note that the matches do not include overlapping matches at V-D or D-J junctions. The default value is 5 nucleotides.
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label class="m blastp" for="D_penalty">D gene mismatch penalty</label>
|
||
<div class="input blastp">
|
||
<span class="nonDefPar">♦<span class="acPromt">D gene mismatch penalty non-default value</span></span>
|
||
<select name="D_penalty" id="D_penalty" class="reset checkDef par" defVal="" >
|
||
<option selected="selected" value="-2" >-2</option>
|
||
<option value="-4" >-4</option>
|
||
<option value="-3" >-3</option>
|
||
<option value="-1" >-1</option>
|
||
</select>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Mismatch penalty for D gene help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
A higher mismatch penalty (for example, -4) favors detecting D gene matches with higher similarity to the query sequence
|
||
but such matched regions are not necessarily long. On the other hand, a lower mismatch penalty (for example, -1) favors
|
||
detecting longer D gene matches that do not necessarily have a high similarity to the query sequence. In general,
|
||
a higher penalty works better if your sequence has few or no somatic mutations. But if your sequence has significant
|
||
mutations (>5%),then a lower penalty should be chosen if you want to accommodate the low similarity introduced by mutations.
|
||
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label for="extend_align5end" class="m ">Alignment extension</label>
|
||
<div class="input ">
|
||
<span class="nonDefPar">♦<span class="acPromt">Alignment at 5' end non-default value</span></span>
|
||
<input type="checkbox" value="true" name="extend_align5end" class="checkDef reset par" id="extend_align5end" defVal="unchecked" />
|
||
<label for="extend_align5end" class="m ">Extend alignment at 5' end</label>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="extend_align5end help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
<p>
|
||
If your sequence has too many differences (due to mutations or other reasons) to the germline sequence at 5' end of the V gene, then IgBLAST result may not show that part of the V gene since IgBLAST uses local alignment algorithm. However, if you'd like to see those missed bases/residues anyway, you can enable this option to direct IgBLAST to perform simple gapless alignment extension (up to 30 bases/residues) into that region. Note that this extension is not a BLAST alignment and should not be used to infer any homology between the query and the subject sequences. It is intended only as a convenience to show the missed part in the context of the germline sequences. If you want to see true BLAST alignment to cover your sequence as much as possible, make sure you select the lowest mismatch penalty (i.e., -1).
|
||
</p>
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label for="extend_align3end" class="m ">Alignment extension</label>
|
||
<div class="input ">
|
||
<span class="nonDefPar">♦<span class="acPromt">Extend alignment at 3' end non-default value</span></span>
|
||
<input type="checkbox" value="true" name="extend_align3end" class="checkDef reset par" id="extend_align3end" defVal="unchecked" />
|
||
<label for="extend_align3end" class="m ">Extend alignment at 3' end</label>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="extend_align3end help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
<p>
|
||
This is same as "Extend alignment at 5' end" except that it extends alignment at 3' end of the J gene up to 15 bps.
|
||
</p>
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label for="detect_overlap" class="m blastp">V(D)J genes overlap</label>
|
||
<div class="input blastp">
|
||
<span class="nonDefPar">♦<span class="acPromt">Allow V(D)J genes to overlap</span></span>
|
||
<input type="checkbox" value="true" name="detect_overlap" class="checkDef reset par" id="detect_overlap" defVal="unchecked" />
|
||
<label for="detect_overlap" class="m blastp">Allow to overlap</label>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="detect_overlap help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
<p>
|
||
Enabling this option allows V(D)J genes to overlap at the rearranging junctions (i.e, there might be a stretch of nucleotide homology that is shared between the V(D)J gene segment ends, which mostly happens when there are no N nucleotide additions). The program does not allow V, D, J genes to overlap when assigning V, D, J gene matches by default. While this option might change the results for D gene matches in some cases, it has no effect on results for V gene matches (as well as related match statistics). Its effect on J gene matches is minimal and only occurs in rare cases. Note that this option is active only when the D and J gene mismatch penalty are set to -4 and -3, respectively.
|
||
|
||
|
||
</p>
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label for="min_V_length" class="m ">Min required V gene length</label>
|
||
<div class="input">
|
||
<span class="nonDefPar">♦<span class="acPromt">Min required V gene length non-default value</span></span>
|
||
<input type="text" name="min_V_length" size="3" value = "" id="min_V_length" defVal="9" class="checkDef reset par"/>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="min_V_length help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
<p>
|
||
Only shows results if the query sequence matches a germline V gene for at least the specified minimal length (i.e., number of bases or amino acids). Otherwise, reports "No hits found".
|
||
</p>
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
<label for="min_J_length" class="m blastp">Min required J gene length</label>
|
||
<div class="input blastp">
|
||
<span class="nonDefPar">♦<span class="acPromt">Min required J gene length non-default value</span></span>
|
||
<input type="text" name="min_J_length" size="3" value = "" id="min_J_length" defVal="0" class="checkDef reset par"/>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="min_J_length help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
<p>
|
||
Only shows results if the query sequence matches a germline J gene for at least the specified minimal length (i.e., number of bases). Otherwise, reports "No hits found".
|
||
</p>
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
<label class="m blastp" for="J_penalty">J gene mismatch penalty</label>
|
||
<div class="input blastp">
|
||
<span class="nonDefPar">♦<span class="acPromt">J gene mismatch penalty non-default value</span></span>
|
||
<select name="J_penalty" id="J_penalty" class="reset checkDef par" defVal="" >
|
||
<option selected="selected" value="-2" >-2</option>
|
||
<option value="-3" >-3</option>
|
||
<option value="-1" >-1</option>
|
||
</select>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Mismatch penalty for J gene help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
A higher mismatch penalty (for example, -3) favors detecting J gene matches with higher similarity to the query sequence
|
||
but such matched regions are not necessarily long. On the other hand, a lower mismatch penalty (for example, -1) favors
|
||
detecting longer matches that do not necessarily have a high similarity to the query sequence. in general,
|
||
a higher penalty works better if your sequence has few or no somatic mutations. But if your sequence has significant
|
||
mutations (>5%),then a lower penalty should be chosen if you want to accommodate the low similarity introduced by mutations.
|
||
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
</fieldset>
|
||
|
||
<span id="diffMes" class="diffMes">Note: Parameter values that differ from the default are highlighted in yellow and marked with
|
||
<span class="nondefMark">♦</span></span>
|
||
<div class="searchInfo ">
|
||
<div class="summary">
|
||
<input type="button" value="Search" class="blastbutton prbutton">
|
||
</div>
|
||
<div class="searchsummary">
|
||
<div class="openNewWin ">
|
||
<input class="newwin checkDef" type="checkbox" name="NEWWIN" id="nw1" form="searchForm" winType="random" defVal="unchecked" />
|
||
<label class="inlineLabel " for="nw1">Show results in a new window</label>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<fieldset class=" section">
|
||
|
||
<legend>Formatting Options</legend>
|
||
|
||
<label class="m" for="num_alignments_V">Number of germline gene</label>
|
||
|
||
<div class="input ">
|
||
<div class=" infl">
|
||
<label for="num_alignments_V">V gene</label>
|
||
<label for="num_alignments_D" class="lbLm blastp">D gene</label>
|
||
<label for="num_alignments_J" class="lbLm blastp">J gene</label>
|
||
<label for="num_alignments_C" class="lbLm blastp germline_db_C">C gene</label>
|
||
</div>
|
||
|
||
<span>
|
||
<span class="nonDefPar">♦<span class="acPromt">Number of germline V gene non-default value</span></span>
|
||
<select name = "num_alignments_V" id="num_alignments_V" class="reset checkDef par" defVal="3">
|
||
<option value="1" >1</option>
|
||
<option value="2" >2</option>
|
||
<option selected="selected" value="3" >3</option>
|
||
<option value="4" >4</option>
|
||
<option value="5" >5</option>
|
||
<option value="10" >10</option>
|
||
<option value="20" >20</option>
|
||
<option value="50" >50</option>
|
||
<option value="100" >100</option>
|
||
</select>
|
||
</span>
|
||
|
||
<span class="rs">
|
||
<span class="nonDefPar">♦<span class="acPromt">Number of germline D gene non-default value</span></span>
|
||
<select name = "num_alignments_D" id="num_alignments_D" class="reset checkDef blastp par" defVal="3">
|
||
<option value="1" >1</option>
|
||
<option value="2" >2</option>
|
||
<option selected="selected" value="3" >3</option>
|
||
<option value="4" >4</option>
|
||
<option value="5" >5</option>
|
||
<option value="10" >10</option>
|
||
<option value="15" >15</option>
|
||
<option value="30" >30</option>
|
||
</select>
|
||
</span>
|
||
|
||
<span class="rs">
|
||
<span class="nonDefPar">♦<span class="acPromt">Number of germline J gene non-default value</span></span>
|
||
<select name = "num_alignments_J" id="num_alignments_J" class="reset checkDef blastp par" defVal="3">
|
||
<option value="1" >1</option>
|
||
<option value="2" >2</option>
|
||
<option selected="selected" value="3" >3</option>
|
||
<option value="4" >4</option>
|
||
<option value="5" >5</option>
|
||
<option value="10" >10</option>
|
||
<option value="15" >15</option>
|
||
</select>
|
||
</span>
|
||
|
||
<span class="rs germline_db_C">
|
||
<span class="nonDefPar">♦<span class="acPromt">Number of germline C gene non-default value</span></span>
|
||
<select name = "num_alignments_C" id="num_alignments_C" class="reset checkDef blastp par" defVal="2">
|
||
<option value="1" >1</option>
|
||
<option selected="selected" value="2" >2</option>
|
||
<option value="2" >3</option>
|
||
<option value="4" >4</option>
|
||
<option value="5" >5</option>
|
||
<option value="10" >10</option>
|
||
<option value="15" >15</option>
|
||
</select>
|
||
</span>
|
||
</div>
|
||
|
||
<label for="translation" class="m blastp">Amino acid translation</label>
|
||
<div class="input blastp">
|
||
<span class="nonDefPar">♦<span class="acPromt">Amino acid translation non-default value</span></span>
|
||
<input type="checkbox" checked="checked" name="translation" value="true" class="checkDef reset par" id="translation" defVal="checked" />
|
||
<label class="right inlinelabel" for="translation">Show amino acid translation</label>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Amino acid translation help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
This will translate your query as well as the top germline sequence and align the amino acid to the second base of a codon.
|
||
The mismatched amino acids in the germline sequence will be colored.
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label class="m" for="domain">V domain delineation system</label>
|
||
<div class="input">
|
||
<span class="nonDefPar">♦<span class="acPromt">V domain delineation system non-default value</span></span>
|
||
<select name="domain" id="domain" class="reset checkDef par" defVal="" >
|
||
<option selected="selected" value="imgt" >IMGT</option>
|
||
<option value="kabat" >KABAT</option>
|
||
</select>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="V domain delineation system help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
The V domain can be delineated using either IMGT system
|
||
<a href="https://www.ncbi.nlm.nih.gov/pubmed?cmd=Retrieve&dopt=Abstract&list_uids=12477501">(Lefranc et al 2003)</a>
|
||
or Kabat system (Kabat et al, 1991, Sequences of Proteins of Immunological Interest,
|
||
National Institutes of Health Publication No. 91-3242, 5th ed., United States Department of Health and Human Services, Bethesda, MD).
|
||
Domain annotation of the query sequence is based on pre-annotated domain information for the best matched germline hit.
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label for="num_clonotype" class="m ">Number of clonotypes to show</label>
|
||
<div class="input">
|
||
<span class="nonDefPar">♦<span class="acPromt">Number of clonotypes to show non-default value</span></span>
|
||
<input type="text" name="num_clonotype" size="3" value = "" id="num_clonotype" defVal="100" class="checkDef reset par"/>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="num_clonotype help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
<p>
|
||
Number of top clonotypes to show. Note this option is applicable only for multiple queries.
|
||
</p>
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label class="m" for="outfmt">Alignment format</label>
|
||
<div class="input">
|
||
<span class="nonDefPar">♦<span class="acPromt">Alignment format non-default value</span></span>
|
||
<select name="outfmt" id="outfmt" class="reset checkDef par" defVal="" >
|
||
<option selected="selected" value="3" >Query-anchored view using dots for identities </option>
|
||
<option value="4" >Query-anchored view using original sequence letters</option>
|
||
<option value="7" >Tabular</option>
|
||
<option value="19" >AIRR rearrangement tabular</option>
|
||
<option value="99" >AIRR rearrangement tabular (save to file)</option>
|
||
</select>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="V domain delineation system help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
AIRR rearrangement tabular:
|
||
<br>
|
||
This is a tab-separated format that the <a href="http://docs.airr-community.org/en/latest/datarep/rearrangements.html">AIRR community </a>has developed for describing Ig/TCR sequences. Essentially this format includes a header line indicating the field names and each subsequent line contains the tab-separated fields for each query sequence. All sequence positions are now 1-based (Previous AIRR specifications use 0-based start and 1-based end sequence coordinate system. But starting on 11/27/2018, all sequence positions were changed to 1-based system per the new AIRR specifications).
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
</fieldset>
|
||
|
||
<fieldset class=" section">
|
||
|
||
<legend> Additional databases</legend>
|
||
|
||
<label class="m" for="additional_db">Database</label>
|
||
<div class="input">
|
||
<span class="nonDefPar">♦<span class="acPromt">Additional databases non-default value</span></span>
|
||
<select name = "additional_db" id="additional_db" class="reset checkDef par" defVal="" >
|
||
<option selected="selected" value = "" >None</option>
|
||
<option value = "nr" >nr</option>
|
||
<option value = "core_nt" >core_nt</option>
|
||
<option value = "refseq_genomes" >RefSeq genome sequences</option>
|
||
<option value = "IG_DB/mammalia_genomes" >mammalian genomes</option>
|
||
<option value = "pat" >patent</option>
|
||
<option value = "pdb" >pdb</option>
|
||
</select>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Additional database help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
nt: GenBank+EMBL+DDBJ+PDB+RefSeq sequences, but excludes EST, STS, GSS, WGS, TSA, patent sequences as well as phase 0, 1, and 2 HTGS sequences. <br><br>
|
||
core_nt: Same as nt except except for the eukaryotic chromosomal sequences that are part of NCBI genome assemblies. <br><br>
|
||
refseq_genomes: NCBI RefSeq genome sequences. <br><br>
|
||
pdb: Sequences from the Protein Data Bank (PDB).<br><br>
|
||
patent: Nucleotide sequences derived from the Patent division of GenBank.<br><br>
|
||
mammalian genomes: NCBI mammal genomes.<br><br>
|
||
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label for="addl_organism" id="orgLbl" class="m">Organism limit<br />
|
||
<span class="hint">Optional</span>
|
||
</label>
|
||
<div class="input">
|
||
<div id="chooseOther" class="all">
|
||
<input name="addl_organism" size="55" type="text" id="addl_organism" value="" data-jigconfig="dictionary:'taxids_sg'" autocomplete="off" class="jig-ncbiautocomplete reset">
|
||
<input id="defaultSgPrompt" type="hidden" value = "Enter organism common name, binomial, or tax id. Only 20 top taxa will be shown" />
|
||
<input id="defaultSgHelp" type="hidden" value = "Start typing in the text box, then select your taxid. Use the 'plus button to add another organism or group, and the 'exclude' checkbox to narrow the subset. The search will be restricted to the sequences in the database that correspond to your subset." />
|
||
<p class="help">
|
||
<span id="suggestPrompt">Enter organism common name, binomial, or tax id. Only 20 top taxa will be shown.</span>
|
||
<a id="selorg" class="helplink jig-ncbitoggler ui-ncbitoggler" data-ncbitoggler-toggles="selorgInf" title="Organism help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
</p>
|
||
</div>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<p class="helpbox ui-ncbitoggler-slave" id="selorgInf">
|
||
<span id="suggestHelp">
|
||
Start typing in the text box, then select your taxid.
|
||
The search will be restricted to the sequences in the database that correspond to your limited subset.
|
||
</span>
|
||
</p>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
|
||
<label for="v_focus" class="m ">V gene only</label>
|
||
<div class="input ">
|
||
<span class="nonDefPar">♦<span class="acPromt">Search V gene only non-default value</span></span>
|
||
<input type="checkbox" checked="checked" value="true" name="v_focus" class="checkDef reset par" id="v_focus" defVal="checked" />
|
||
<label for="v_focus" class="m ">Search V gene only</label>
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Focus on the V gene help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
<p>
|
||
This allows a user to find the best matches for the V gene in your query sequence among additional non-germline databases
|
||
(i.e., nt, genome, etc). This option has NO effect on search against germline gene databases (see explanation below).
|
||
</p>
|
||
<p>
|
||
A typical rearranged query sequence includes a leader, the V, D, J gene (sometimes the C region is also included).
|
||
When a sequence is submitted for blast search, the similarity matches will be performed over the entire query sequence.
|
||
Unlike the germline V gene database which only contains the V gene sequences, other databases such as nt contain many
|
||
rearranged sequences that also include a leader, the V, D, J and C genes. As a result, the best hit from these
|
||
databases does not necessarily have the best match to the query V gene; Rather, it has the
|
||
best match over the entire query sequence (For example, it may have very high similarity to the
|
||
leader, D, J or C genes in a query sequence but only a low match to the V gene).
|
||
This is not a problem if the goal is trying to find the best overall matches to a query sequence.
|
||
However, if the goal is to find best matches to the V gene of a query sequence, then one needs to
|
||
isolate the V gene part manually from a query sequence and then use it for a search.
|
||
</p>
|
||
<p>
|
||
With this option on, the V gene part from a query sequence is automatically isolated
|
||
(based on comparison to hits from the germline V gene database) and then used for search against additional
|
||
databases like nt. This option should be disabled, however, if the search intention is to find best hits
|
||
based on overall matches.
|
||
</p>
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
<label class="m" for="num_alignments_additional">Number of alignments</label>
|
||
<div class="input">
|
||
<span class="nonDefPar">♦<span class="acPromt">Number of alignments non-default value</span></span>
|
||
<select name = "num_alignments_additional" id="num_alignments_additional" class="reset checkDef par" defVal="10">
|
||
<option value="1" >1</option>
|
||
<option value="5" >5</option>
|
||
<option selected="selected" value="10" >10</option>
|
||
<option value="25" >25</option>
|
||
<option value="50" >50</option>
|
||
<option value="100" >100</option>
|
||
<option value="200" >200</option>
|
||
</select>
|
||
</div>
|
||
|
||
<label class="m" for="evalue">Expect</label>
|
||
<div class="input">
|
||
<span class="nonDefPar">♦<span class="acPromt">Expect non-default value</span></span>
|
||
<select name="evalue" id="evalue" class="reset checkDef par" defVal="1" >
|
||
<option value="1000" >1000</option>
|
||
<option value="100" >100</option>
|
||
<option selected="selected" value="1" >1</option>
|
||
<option value="1e-5" >1e-5</option>
|
||
<option value="1e-20" >1e-20</option>
|
||
<option value="1e-50" >1e-50</option>
|
||
</select>
|
||
|
||
<a class="helplink jig-ncbitoggler ui-ncbitoggler" title="Focus on the V gene help" href="#"><i class="fas fa-question-circle"></i> <span class="usa-sr-only">Help</span></a>
|
||
<div class="ui-helper-reset" aria-live="assertive" >
|
||
<div class="helpbox ui-ncbitoggler-slave">
|
||
This is the statistical significance threshold for reporting matches against database sequences. Lower EXPECT thresholds are more stringent and report only high similarity matches. Choose higher EXPECT value (for example 1 or more) if you expect a low identity between your query sequence and the targets. Note that this option is only for the additional database search (it has no effect on the germline gene database search).
|
||
|
||
|
||
|
||
</p>
|
||
</div>
|
||
</div><!-- ARIA -->
|
||
</div>
|
||
|
||
</fieldset>
|
||
|
||
|
||
|
||
</div> <!-- query -->
|
||
|
||
<div class="searchInfo ">
|
||
<div class="summary">
|
||
<input type="button" value="Search" class="blastbutton prbutton">
|
||
</div>
|
||
<div class="searchsummary">
|
||
<div class="openNewWin ">
|
||
<input class="newwin checkDef" type="checkbox" name="NEWWIN" id="nw2" form="searchForm" winType="random" defVal="unchecked" />
|
||
<label class="inlineLabel " for="nw2">Show results in a new window</label>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<input name="LINK_LOC" id="LINK_LOC" type="hidden" value="" />
|
||
<input id="searchType" type="hidden" name="SEARCH_TYPE" value="IG" />
|
||
<input type="hidden" name="igsource" value="new">
|
||
<input type="hidden" name="analyze" value="on">
|
||
<input name="CMD" id="cmd" type="hidden" value="request" />
|
||
<!-- the field that will keep the number of differemces from default params the first for all -->
|
||
<input type="hidden" value="0" id="NUM_DIFFS"/>
|
||
<!-- the second only for options -->
|
||
<input type="hidden" value="0" id="NUM_OPTS_DIFFS"/>
|
||
<div id="savedLists" class="hidden">
|
||
<select id="germline_db_V_human"><option selected="selected" class="Deflt" value="IG_DB/imgt.Homo_sapiens.V.f.orf.p" >IMGT human V genes (F+ORF+in-frame P)</option>
|
||
<option value="IG_DB/airr_c_human_ig.V" >AIRR-C human germline V gene set</option>
|
||
<option value="IG_DB/human_gl_V" >NCBI human V genes</option>
|
||
<option value="IG_DB/imgt.Homo_sapiens.V.f.orf" >IMGT human V genes (F+ORF)</option>
|
||
<option value="IG_DB/imgt.Homo_sapiens.V.p" >IMGT human V genes (In-frame P)</option>
|
||
<option value="IG_DB/imgt.Homo_sapiens.V.f.orf.p.include_orp" >IMGT human V genes (F+ORF+in-frame P) including orphons</option>
|
||
<option value="IG_DB/imgt.Homo_sapiens.V.f.orf.include_orp" >IMGT human V genes (F+ORF) including orphons</option>
|
||
<option value="IG_DB/imgt.Homo_sapiens.V.p.include_orp" >IMGT human V genes (In-frame P) including orphons</option>
|
||
<option value="IG_DB/human_gl_V.old" >NCBI human V genes (old)</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_D_human"><option selected="selected" class="Deflt" value="IG_DB/imgt.Homo_sapiens.D.f.orf" >IMGT human D genes (F+ORF)</option>
|
||
<option value="IG_DB/airr_c_human_igh.D" >AIRR-C human germline D gene set</option>
|
||
<option value="IG_DB/imgt.Homo_sapiens.D.f.orf.include_orp" >IMGT human D genes (F+ORF) including orphons</option>
|
||
<option value="IG_DB/human_gl_D.old" >NCBI human D genes (old)</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_J_human"><option selected="selected" class="Deflt" value="IG_DB/imgt.Homo_sapiens.J.f.orf" >IMGT human J genes (F+ORF)</option>
|
||
<option value="IG_DB/airr_c_human_ig.J" >AIRR-C human germline J gene set</option>
|
||
<option value="IG_DB/human_gl_J.old" >NCBI human J genes (old)</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_C_human"><option selected="selected" class="Deflt" value="" >None</option>
|
||
<option value="IG_DB/ncbi_human_c_genes" >NCBI human C genes</option>
|
||
<option value="IG_DB/imgt.Homo_sapiens.C" >IMGT human C genes</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_V_mouse"><option selected="selected" class="Deflt" value="IG_DB/imgt.Mus.V.f.orf.p" >IMGT mouse V genes (F+ORF+in-frame P)</option>
|
||
<option value="IG_DB/imgt.Mus.V.f.orf" >IMGT mouse V genes (F+ORF)</option>,
|
||
<option value="IG_DB/imgt.Mus.V.p" >IMGT mouse V genes (In-frame P)</option>,
|
||
<option value="IG_DB/imgt.Mus.V.f.orf.p.include_orp" >IMGT mouse V genes (F+ORF+in-frame P) including orphons</option>,
|
||
<option value="IG_DB/imgt.Mus.V.f.orf.include_orp" >IMGT mouse V genes (F+ORF) including orphons</option>,
|
||
<option value="IG_DB/airr_c_balbc.V" >AIRR-C BALB/c mouse IGHV genes</option>,
|
||
<option value="IG_DB/airr_c_BALB_c_ByJ.V" >AIRR-C BALB/c/ByJ mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_C57BL_6.V" >AIRR-C C57BL/6 mouse IGHV genes</option>,
|
||
<option value="IG_DB/airr_c_C57BL_6J.V" >AIRR-C C57BL/6J mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_129S1_SvImJ.V" >AIRR-C 129S1/SvImJ mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_A_J.V" >AIRR-C A/J mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_AKR_J.V" >AIRR-C AKR/J mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_C3H_HeJ.V" >AIRR-C C3H/HeJ mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_CAST_EiJ.V" >AIRR-C CAST/EiJ mouse IGHV+IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_CBA_J.V" >AIRR-C CBA/J mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_DBA_1J.V" >AIRR-C DBA/1J mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_DBA_2J.V" >AIRR-C DBA/2J mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_LEWES_EiJ.V" >AIRR-C LEWES/EiJ mouse IGHV+IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_MRL_MpJ.V" >AIRR-C MRL/MpJ mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_MSM_MsJI.V" >AIRR-C MSM/MsJI mouse IGHV+IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_NOD_ShiLtJ.V" >AIRR-C NOD/ShiLtJ mouse IGHV+IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_NOR_LtJ.V" >AIRR-C NOR/LtJ mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_NZB_BlNJ.V" >AIRR-C NZB/BlNJ mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_PWD_PhJ.V" >AIRR-C PWD/PhJ mouse IGHV+IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/airr_c_SJL_J.V" >AIRR-C SJL/J mouse IGKV+IGLV genes</option>,
|
||
<option value="IG_DB/mouse_gl_V" >NCBI mouse V genes</option>,
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_D_mouse"><option selected="selected" class="Deflt" value="IG_DB/imgt.Mus.D.f.orf.p" >IMGT Mouse D genes (F+ORF+in-frame P)</option>
|
||
<option value="IG_DB/imgt.Mus.D.f.orf" >IMGT Mouse D genes (F+ORF)</option>
|
||
<option value="IG_DB/imgt.Mus.D.p" >IMGT Mouse D genes (In-frame P)</option>
|
||
<option value="IG_DB/mouse_gl_D" >NCBI mouse D genes</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_J_mouse"><option selected="selected" class="Deflt" value="IG_DB/imgt.Mus.J.f.orf.p" >IMGT mouse J genes (F+ORF+in-frame P)</option>
|
||
<option value="IG_DB/imgt.Mus.J.f.orf" >IMGT mouse J genes (F+ORF)</option>
|
||
<option value="IG_DB/imgt.Mus.J.p" >IMGT mouse J genes (In-frame P)</option>
|
||
<option value="IG_DB/mouse_gl_J" >NCBI mouse J genes</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_C_mouse"><option selected="selected" class="Deflt" value="" >None</option>
|
||
<option value="IG_DB/imgt.Mus.C" >IMGT mouse C genes</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_V_rat"><option selected="selected" class="Deflt" value="IG_DB/imgt.Rattus_norvegicus.V.f.orf.p" >IMGT rat V genes (F+ORF+in-frame P)</option>
|
||
<option value="IG_DB/imgt.Rattus_norvegicus.V.f.orf" >IMGT rat V genes (F+ORF)</option>
|
||
<option value="IG_DB/imgt.Rattus_norvegicus.V.p" >IMGT rat V genes (In-frame P)</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_D_rat"><option selected="selected" class="Deflt" value="IG_DB/imgt.Rattus_norvegicus.D.f.orf" >IMGT rat D genes (F+ORF)</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_J_rat"><option selected="selected" class="Deflt" value="IG_DB/imgt.Rattus_norvegicus.J.f.orf" >IMGT rat J genes (F+ORF)</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_C_rat"><option selected="selected" class="Deflt" value="" >None</option></select>
|
||
<select id="germline_db_V_rabbit"><option selected="selected" class="Deflt" value="IG_DB/imgt.Oryctolagus_cuniculus.V.f.orf.p" >IMGT rabbit V genes (F+ORF+in-frame P)</option>
|
||
<option value="IG_DB/imgt.Oryctolagus_cuniculus.V.f.orf" >IMGT rabbit V genes (F+ORF)</option>
|
||
<option value="IG_DB/imgt.Oryctolagus_cuniculus.V.p" >IMGT rabbit V genes (In-frame P)</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_D_rabbit"><option selected="selected" class="Deflt" value="IG_DB/imgt.Oryctolagus_cuniculus.D.f.orf" >IMGT rabbit D genes (F+ORF)</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_J_rabbit"><option selected="selected" class="Deflt" value="IG_DB/imgt.Oryctolagus_cuniculus.J.f.orf" >IMGT rabbit J genes (F+ORF)</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_C_rabbit"><option selected="selected" class="Deflt" value="" >None</option></select>
|
||
<select id="germline_db_V_rhesus_monkey"><option selected="selected" class="Deflt" value="IG_DB/rhesus_monkey_V" >rhesus monkey germline IGHV genes</option>
|
||
<option value="IG_DB/imgt.Macaca_mulatta.V.f.orf.p" >IMGT rhesus monkey V genes (F+ORF+in-frame P)</option>
|
||
<option value="IG_DB/imgt.Macaca_mulatta.V.f.orf" >IMGT rhesus monkey V genes (F+ORF)</option>
|
||
<option value="IG_DB/imgt.Macaca_mulatta.V.p" >IMGT rhesus monkey V genes (In-frame P)</option>
|
||
<option value="custom" >Custom</option></select>
|
||
<select id="germline_db_D_rhesus_monkey"><option selected="selected" class="Deflt" value="IG_DB/rhesus_monkey_D" >rhesus monkey germline D genes</option>
|
||
<option value="IG_DB/imgt.Macaca_mulatta.D.f.orf" >IMGT rhesus monkey germline D genes (F+ORF)</option>
|
||
<option value="custom" >Custom</option></select>
|
||
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