459 lines
19 KiB
HTML
459 lines
19 KiB
HTML
<html><!-- #BeginTemplate "/Templates/dbSNP_new.dwt" --><!-- DW6 --><head>
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<title>dbSNP Batch Query</title>
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<META name="keywords" content="single nucleotide polymorphism, SNP,
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sequence variation, genome, gene mapping, population structure, dbSNP,
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biotechnology information, ncbi, national library of medicine, nlm, database,
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<META name="description" content="The Single Nucleotide Polymorphism
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database (dbSNP) is a public-domain archive for a broad collection of simple
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genetic polymorphisms.">
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<META name="author" content="snpdev">
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<link rel="stylesheet" href="/corehtml/ncbi.css">
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<link rel="stylesheet" href="snp.css" type="text/css">
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<body>
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<td><table width="100%" border="0" cellpadding="0" cellspacing="0">
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<tr>
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<td width="135" align="left" bgcolor="#336699"><a href=""><img src="corehtml/left.GIF" width="130" height="45" border="0" alt="NCBI"></a><br>
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</td>
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<td align="left"><img name="SNPlogo" src="Images/SNPlogo2_ver2.jpg" width="440" height="70" border="0" alt="dbSNP"></p></td>
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<tr>
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<td><table class="TEXT" border="0" cellspacing="0" cellpadding="2" bgcolor="#000000" width="100%">
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<tr class="TEXT" align="CENTER">
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<td><a href="/dbvar" title="Database of Structural Variations" class="topbarHeading"><font color="#FFFFFF">dbVar</font></a></td>
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<td><a href="/clinvar" title="Database of human variations and phenotypes" class="topbarHeading"><font color="#FFFFFF">ClinVar</font></a></td>
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<td><a href="/gap" title="Database of Genotypes and Phenotypes" class="topbarHeading"><font color="#FFFFFF">GaP</font></a></td>
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<td><a href="/entrez/query.fcgi?db=PubMed" class="topbarHeading"><font color="#FFFFFF">PubMed</font></a></td>
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<td><a href="/entrez/query.fcgi?db=Nucleotide" class="topbarHeading"><font color="#FFFFFF">Nucleotide</font></a></td>
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<td><a href="/entrez/query.fcgi?db=Protein" class="topbarHeading"><font color="#FFFFFF">Protein</font></a></td>
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<form method="post" name="searchform" id="SearchDb">
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<tbody>
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<tr>
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<td class="SMALL1"><div id="HintEntrezSnp" class="hintBox">Search small variations in dbSNP or large structural variations in dbVar</div>
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<label for="Search"> Search Entrez</label>
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<small>
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<select id="db_select" >
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<option value="/snp" selected>dbSNP</option>
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<option value="/dbvar" >dbVar</option>
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</small>
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<label for="term">for</label>
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<input type="text" name="term" id="entrez_term" alt="search term" size="24" onkeypress="inputKeyPress(event, this);">
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<div align="center"></div>
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<div align="center"><!-- #BeginLibraryItem "/Library/FAQ search box.lbi" -->
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<div class="roundcont">
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<div class="faqtitle">Have a question about dbSNP? Try searching the SNP FAQ Archive!</div>
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<form name="frmGo" method="get" action="/entrez/query.fcgi" onSubmit="searchFAQ(this);">
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<input name="db" value="Books" type="hidden">
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<input name="cmd" value="Search" type="hidden">
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<input name="term" value="" alt="FAQ search Term" size="12">
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<input type="submit" name="Submit" value="Go">
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<input name="doptcmdl" value="TOCView" type="hidden">
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</form>
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<script language="JavaScript" type="text/JavaScript">
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<!--
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function searchFAQ (frm) {
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frm.term.value += ' AND helpsnpfaq[book]';
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}
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-->
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</script>
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</div> <!-- #EndLibraryItem --></div><div class="sidebarDiv" id="sideBar">
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<p>
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<div class="sidebarHeading" id="divGeneral" onClick="toggleSideBar(this);" onKeyPress="toggleSideBar(this);">GENERAL</div>
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<div class="sidebarSubHeadingDiv" id="divGeneralContent">
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<a accesskey="R" href="/feed/rss.cgi?ChanKey=dbsnpnews">RSS Feed</a><a href="/feed/rss.cgi?ChanKey=dbsnpnews"><img src="Images/rss.gif" alt="RSS" border="0"></a><br>
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<a accesskey="A" href="javascript:Help();" >Contact Us</a><br>
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<a accesskey="B" href="/dbvar/content/org_summary/" >Organism Data</a><br>
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<a accesskey="C" href="index.html">dbSNP Homepage</a><br>
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<a accesskey="V" href="/variation/">NCBI Variation Resources</a><br>
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<a accesskey="D" href="/mailman/listinfo/dbsnp-announce">Announcements</a><BR>
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<a accesskey="E" href="snp_summary.cgi">dbSNP Summary</a><BR>
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<a accesskey="F" href="ftp://ftp.ncbi.nih.gov/snp/">FTP Download</a></div>
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<div class="sidebarHeading" id="divSubmission" onClick="toggleSideBar(this);" onKeyPress="toggleSideBar(this);">SNP SUBMISSION</div>
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<div class="sidebarSubHeadingDiv" id="divSubmissionContent">
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<a accesskey="J" href="/snp/docs/submission/hts_launch_and_introductory_material/">How to Submit</a><br>
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<a accesskey="K" href="handle.html">Handle Request</a><br>
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</div>
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<div class="sidebarHeading" id="divDocumentation" onClick="toggleSideBar(this);" onKeyPress="toggleSideBar(this);">DOCUMENTATION</div>
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<div class="sidebarSubHeadingDiv" id="divDocumentationContent">
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<a accesskey="S" href="ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_SNP.pdf">dbSNP Fact Sheet</a><img src="new.gif" width="25" height="12" alt="NEW gif"><BR>
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<br>
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<a accesskey="M" href="buildhistory.cgi">Build History</a><br>
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<a accesskey="N" href="/books/NBK3848/" title="Search SNP archived FAQ updated to 2006">Search FAQ Archive</a><br>
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<a accesskey="O" href="/books/NBK174586/">dbSNP Handbook</a><br>
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<a accesskey="P" href="get_html.cgi?whichHtml=overview">Overview</a><br>
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<a accesskey="Q" href="/About/primer/snps.html">SNP Science Primer</a><br>
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<a accesskey="S" href="ftp://ftp.ncbi.nih.gov/snp/database/b124/mssql/schema/erd_dbSNP.pdf">Database Schema</a><br>
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<a accesskey="T" href="snp_db_list_table.cgi">Database Dictionary</a><br>
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<a acceskey="U" href="snp_schemaChange.htm">Database Changes</a><br>
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<a acceskey="V" href="/SNP/geno/genoex_doc.html">Genotype Schema</a><br>
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<a acceskey="W" href="ftp://ftp.ncbi.nih.gov/snp/00readme.txt">Data Formats</a><BR>
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<a acceskey="X" href="docsum/docsum_doc.html">Docsum Schema</a><BR>
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<a acceskey="Y" href="Hetfreq.html">Heterozygosity Computation</a>
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</div>
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<div class="sidebarHeading" id="divSearch" onClick="toggleSideBar(this);" onKeyPress="toggleSideBar(this);">SEARCH</div>
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<div class="sidebarSubHeadingDiv" id="divSearchContent">
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<a acceskey="R" href="/variation/tools/reporter">Variation Reporter</a><br>
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<a acceskey="R" href="/variation/view/?q=CFH">Variation Viewer</a><br>
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<a acceskey="Z" href="/snp">Entrez SNP</a><br>
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<a acceskey="1" href="SNPeutils.htm">EUtils API</a><br>
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<a accesskey="2" href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_SPEC=SNP&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=dbSNP_homepage">Blast SNP</a><br>
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<a accesskey="3" href="batchquery.html">Batch Query</a><BR>
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<a accesskey="5" href="snp_gf.cgi">Genotype Query</a><BR>
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<a accesskey="6" href="snp_tableList.cgi?type=submitter">By Submitter</a><BR>
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<a accesskey="7" href="snp_batchSearch.cgi?init=y">New Batches</a><BR>
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<a accesskey="8" href="snp_tableList.cgi?type=method">Method</a><br>
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<a accesskey="9" href="snp_tableList.cgi?type=pop">Population Detail</a><br>
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<!-- <a accesskey="Q" href="../popclass.cgi">Population Class</a><br> -->
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<a accesskey="]" href="snp_tableList.cgi?type=pub">Publication</a><br>
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</div>
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<!--
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<div class="sidebarHeading" id="divHaplotype" onClick="toggleSideBar(this);" onKeyPress="toggleSideBar(this);">HAPLOTYPE</div>
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<div class="sidebarSubHeadingDiv" id="divHaplotypeContent">
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<a href="../hap/dbSNP_haplotype_intro.html">Submission</a>
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</div>
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-->
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<div class="sidebarHeading" id="divRelatedSites" onClick="toggleSideBar(this);" onKeyPress="toggleSideBar(this);">RELATED SITES</div>
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<div class="sidebarSubHeadingDiv" id="divRelatedSitesContent">
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<a accesskey="=" href="/variation/">NCBI Variation resources</a><br>
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<a accesskey="-" href="/sites/entrez?db=dbvar">dbVar</a><br>
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<a accesskey="-" href="/sites/entrez?db=gap">dbGaP</a><br>
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<a accesskey="-" href="/clinvar/">ClinVar</a><br>
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<a accesskey="-" href="/gtr/">GTR</a><br>
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<a accesskey=";" href="/mhc/MHC.fcgi?cmd=init">dbMHC</a></div>
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</div>
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</td>
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</tr>
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</table>
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<script language="JavaScript" type="text/JavaScript">
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toggleSideBar($('divGeneral'));
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</script>
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<noscript>See Human Variations Search</noscript><!-- #EndLibraryItem --><SPAN class="GUTTER1"><BR>
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</SPAN> </td>
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<td width="5"> <img src="corehtml/spacer10.GIF"
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width="3" height="1" border="0" alt="Spacer gif"> </td>
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<!-- #BeginEditable "SNP_right column" -->
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<!-- SNP BATCH STARTS HERE -->
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<td width="460"><p><strong>dbSNP BATCH QUERY</strong><br>
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<br>
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dbSNP batch query allows you to retrieve
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a large number of SNPs in a batch using dbSNP accessions for individual
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submissions (ss#), submitter id's (handle|local_snp_id), or dbSNP RefSNP
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cluster ID's (rs#). <font color="#0000FF">Batch query also accept </font><font color="#0000FF">results</font><font color="#0000FF">
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from <a href="/entrez/query.fcgi?db=Snp&cmd=Limits">Entrez
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SNP</a> (Select Display->dbSNP Batch Report) </font>. You will be notified by email when your
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query is done with instructions for retrieving the result. There are two
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ways to submit the query from dbSNP:</p>
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<table width="92%" border="0">
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<tr>
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<td width="6%" valign="top"><b>(1)</b></td>
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<td width="94%" valign="top">Select "Enter #" as a submission format
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below and enter the numbers directly on the next web page .</td>
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</tr>
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<tr>
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<td width="6%" valign="top" height="227"><b>(2)</b></td>
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<td width="94%" height="227" valign="top">
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<div align="left">Select "Upload #" as a submission format below and upload a
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text file containing a list of SNP IDs on the upload web page. This
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query will accept lists generated by the users (Formatting instructions
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below) or result set downloaded from dbSNP or <a href="/entrez/query.fcgi?db=Snp&cmd=Limits">Entrez
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SNP</a> (See sidebar and <a href="EntrezBatchHelp.htm">instruction</a>).</div>
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<table width="89%" border="0">
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<tr>
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<td width="5%" valign="top"> </td>
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<td width="5%" valign="top"><b></b></td>
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<td width="95%" valign="top"><b>File formatting instructions:</b></td>
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</tr>
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<tr>
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<td width="5%" valign="top"> </td>
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<td width="5%" valign="top"><b>a.</b></td>
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<td width="95%" valign="top">The list can only contain one type
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of entry, either rs, ss, or local snp ID.</td>
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</tr>
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<tr>
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<td width="5%" valign="top"> </td>
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<td width="5%" valign="top"><b>b.</b></td>
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<td width="95%" valign="top">Each entry must contain the identifier
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prefix "ss" or "rs" (ie. ss23411 or rs23424) or the handle of
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the submitting lab and a vertical bar followed by the local
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snp ID (i.e. TSC-CSHL|TSC0000026).</td>
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</tr>
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<tr>
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<td width="5%" valign="top"> </td>
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<td width="5%" valign="top"><b>c.</b></td>
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<td width="95%" valign="top"> The entries does not have to be
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ordered, but they are limited to one per line.</td>
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</tr>
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<tr>
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<td width="5%" valign="top"> </td>
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<td width="5%" valign="top"><b>d.</b></td>
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<td width="95%" valign="top">Save the list as a text file.</td>
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</tr>
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<tr>
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<td width="5%" valign="top" height="12"> </td>
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<td width="5%" valign="top" height="12"><b>e.</b></td>
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<td width="95%" valign="top" height="12">
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<p>Example:</p>
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</td>
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</tr>
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<tr>
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<td width="5%" valign="top"> </td>
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<td width="5%" valign="top"><b></b></td>
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<td width="95%" valign="top">ss34</td>
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</tr>
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<tr>
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<td width="5%" valign="top"> </td>
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<td width="5%" valign="top"><b></b></td>
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<td width="95%" valign="top">ss35</td>
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</tr>
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<tr>
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<td width="5%" valign="top"> </td>
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<td width="5%" valign="top"><b></b></td>
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<td width="95%" valign="top">ss12</td>
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</tr>
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<tr>
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<td width="5%" valign="top"> </td>
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<td width="5%" valign="top"><b></b></td>
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<td width="95%" valign="top">ss9</td>
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</tr>
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<tr>
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<td width="5%" valign="top"> </td>
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<td width="5%" valign="top"><b></b></td>
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<td width="95%" valign="top">ss100</td>
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</tr>
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</table>
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</td>
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</tr>
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</table>
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<p> To begin, choose a type of submission format below and you will be directed
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to the correct web submission form for entering your email, SNP IDs, and
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output format. </p>
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<form name="jump">
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<p>
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<select name="menu" onChange="location=document.jump.menu.options[document.jump.menu.selectedIndex].value;" value="GO">
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<option value="./batchquery.html" selected>Submission Format</option>
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<option value="./batchquery.html">-------------------</option>
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<option value="./dbSNP.cgi?list=sslist">Enter SS#</option>
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<option value="./dbSNP.cgi?list=rslist">Enter RS#</option>
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<!-- <option value="./dbSNP.cgi?list=genelist">Enter Gene ID</option> -->
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<option value="./dbSNP.cgi?list=loc_snp_id">Enter local snp ID</option>
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<option value="./dbSNP.cgi?list=crlist">Enter Celera ID</option>
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<!-- <option value="./dbSNP.cgi?list=sub_handle">Enter Handles</option> -->
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<option value="./dbSNP.cgi?list=ssfile">Upload SS#</option>
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<option value="./dbSNP.cgi?list=rsfile">Upload RS#</option>
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<!-- <option value="./dbSNP.cgi?list=genefile">Upload Gene ID</option> -->
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<option value="./dbSNP.cgi?list=loc_snp_idf">Upload local snp ID</option>
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<option value="./dbSNP.cgi?list=crfile">Upload Celera ID</option>
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<!-- <option value="./dbSNP.cgi?list=sub_handlef">Upload Handles</option> -->
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</select>
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</p>
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</form>
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<!-- SNP BATCH ENDS HERE -->
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<P> </P><!-- #BeginLibraryItem "/Library/dbSNPTextLinks.lbi" -->
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<!--Bottom Link Start -->
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<!--Bottom Link Start -->
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NCBI: <a href="/About/disclaimer.html"
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class="SMALL1">Disclaimer</a> <a
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href="/About/privacy.html"
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class="SMALL1">Privacy statement</a></p>
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<!-- #EndLibraryItem --><!-- #EndEditable --> <br>
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</tr>
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</table>
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<!-- end of content -->
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</body>
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<!-- the header -->
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<!-- #EndTemplate --></html>
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