BLAST: Basic Local Alignment Search Tool

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The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. <a id="moreHelp" class="helplink ui-ncbitoggler" data-jig="ncbitoggler" data-jigconfig="isIcon:false" data-ncbitoggler-toggles="hpHelp" title="help" href="#">Learn more</a> </span> <div class="ui-helper-reset" aria-live="assertive" > <div class="helpbox ui-ncbitoggler-slave" id="hpHelp"> The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. </div> </div> </div> <div class="newsbox">  <div class="featurebox"> <h3>News</h3> <dl> <dt>Non-interactive searches of nt switch to core_nt</dt> <dd> <br> <div> <div><p>Starting late September 2024 all non-interactive WebBLAST and PrimerBLAST searches of ``nt`` will</p><br></div> Tue, 24 Sep 2024 </dd> </dl> <p><a class="morelink" href="../../doc/blast-news/2024-BLAST-News.html">More BLAST news...</a></p> </div> </div> </div> <div id="chooseprog" class="section clearfix"> <h2>Web BLAST</h2> <a href="Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome" class="left spFirst" id="homeBlastn" title="Nucleotide BLAST"><img alt="Nucleotide query->Nucleotide database" src="images/nucleutide-blast-cover.png"/></a> <div id="transl" class="left"> <a href="Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome" id="homeBlastx" title="blastx"><img class="" alt="Translated Nucleotide query->Protein database" src="images/blastx-arrow.png"/></a> <a href="Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome" id="homeTblastn" title="tblastn"><img class="" alt="Protein query->Translated Nucleotide database" src="images/tblastn-arrow.png"/></a> </div> <a href="Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome" class="left" id="homeBlastp" title="Protein BLAST"><img alt="Protein query->Protein database" src="images/protein-blast-cover.png"/></a> </div> <div id="gn_search"> <form id="fgs" action="Blast.cgi" method="post"> <h3><label for="qorganism" class="bl" id="srchEuk">BLAST Genomes</label></h3> <input name="TAXID" size="55" type="text" topoption="" id="qorganism" value="" data-jigconfig="dictionary:'bdb_euk_ref_viruses_rep_genomes_sg',isCrossDomain:false" autocomplete="off" data-jig="ncbiautocomplete" class="reset bl" suggesthint="Enter organism common name, scientific name, or tax id"/> <input id="srchDB" type="button" value="Search"/> <input name="PAGE_TYPE" type="hidden" value="BlastSearch" /> <input name="SEARCH_INIT" type="hidden" value="ReprGenomeDBSearch" /> <input name="LINK_LOC" type="hidden" value="blasthomeDBSearch" /> <div id="dbStatInfo"></div> <p class="help hidden" id="sgHelp"> <span id="suggestPrompt"> Enter organism common name, scientific name, or tax id. </span> </p> </form> <ul> <li><a href="Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=OGP__9606__9558&LINK_LOC=blasthome" title="BLAST human genome">Human</a></li> <li><a href="Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=OGP__10090__9559&LINK_LOC=blasthome" title="BLAST mouse genome">Mouse</a></li> <li><a href="Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=OGP__10116__10621&LINK_LOC=blasthome" title="BLAST rat genome">Rat</a></li> <li><a href="Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes" title="BLAST microbial genomes">Microbes</a></li> </ul> </div> </div> <div class="perksblast section"> <h2>Standalone and API BLAST</h2> <ul> <li> <a class="prksLink" href="https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html" title="Download Blast"> <div id="dwnld-bg-img" class="bg-img"> <div class="prksTitle">Download BLAST</div> <div class="prksDescr">Get BLAST databases and executables</div> </div> </a> </li> <li> <a class="prksLink" href="https://blast.ncbi.nlm.nih.gov/doc/blast-help/developerinfo.html" title="Develop Blast"> <div id="dev-bg-img" class="bg-img"> <div class="prksTitle">Use BLAST API</div> <div class="prksDescr">Call BLAST from your application</div> </div> </a> </li> <li> <a class="prksLink" href="https://blast.ncbi.nlm.nih.gov/doc/blast-help/cloudblast.html#cloudblast" title="Cloud Blast"> <div id="cloud-bg-img" class="bg-img"> <div class="prksTitle">Use BLAST in the cloud</div> <div class="prksDescr">Start an instance at a cloud provider</div> </div> </a> </li> </ul> </div> <div class="links section"> <h2>Specialized searches</h2> <ul> <li class="spFirst"><a class="spLink" href="https://blast.ncbi.nlm.nih.gov/smartblast/?LINK_LOC=BlastHomeLink" title="SmartBlast"> <div class="specblast-bg-img"> <div class="spTitle">SmartBLAST</div> <div class="spDesc">Find proteins highly similar to your query</div> </div> </a> </li> <li><a class="spLink" <a href="https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome" title="Find primers"> <div class="specblast-bg-img"> <div class="spTitle">Primer-BLAST</div> <div class="spDesc">Design primers specific to your PCR template</div> </div> </a> </li> <li><a class="spLink" href="Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=blastn&BLAST_SPEC=GlobalAln&LINK_LOC=BlastHomeLink" title="Global alignment"> <div class="specblast-bg-img"> <div class="spTitle">Global Align</div> <div class="spDesc">Compare two sequences across their entire span (Needleman-Wunsch)</div> </div> </a> </li> <li><a class="spLink"href="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi" title="Search conserved domains on a protein"> <div class="specblast-bg-img"> <div class="spTitle">CD-search</div> <div class="spDesc">Find conserved domains in your sequence</div> </div> </a> </li> <li class="spFirst"><a class="spLink"href="https://www.ncbi.nlm.nih.gov/igblast/" title="Search immunoglobulins"> <div class="specblast-bg-img"> <div class="spTitle">IgBLAST</div> <div class="spDesc">Search immunoglobulins and T cell receptor sequences</div> </div> </a> </li> <li> <a class="spLink"href="https://www.ncbi.nlm.nih.gov/tools/vecscreen/" title="Screen a Sequence Using VecScreen"> <div class="specblast-bg-img"> <div class="spTitle">VecScreen</div> <div class="spDesc">Search sequences for vector contamination</div> </div> </a> </li> <li><a class="spLink"href="https://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rps" title="Find a protein sequence's domain architecture"> <div class="specblast-bg-img"> <div class="spTitle">CDART</div> <div class="spDesc">Find sequences with similar conserved domain architecture</div> </div> </a> </li> <li> <a class="spLink"title="Compute a multiple protein sequence alignment" href="https://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi?LINK_LOC=BlastHomeLink"> <div class="specblast-bg-img"> <div class="spTitle">Multiple Alignment</div> <div class="spDesc">Align sequences using domain and protein constraints</div> </div> </a> </li> </ul> </div> </div> </div> </div> <footer> <section class="icon-section"> <div id="icon-section-header" class="icon-section_header">Follow NCBI</div> <div class="grid-container container"> <div class="icon-section_container"> <a class="footer-icon" id="footer_twitter" href="https://twitter.com/ncbi" aria-label="Twitter"><svg data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 300 300"> <defs> <style> .cls-11 { fill: #737373; } </style> </defs> <title>Twitter</title> <path 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