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<meta name="robots" content="INDEX,FOLLOW,NOARCHIVE" /><meta name="citation_inbook_title" content="BLAST® Help [Internet]" /><meta name="citation_title" content="BLAST Help Manual Overview" /><meta name="citation_publisher" content="National Center for Biotechnology Information (US)" /><meta name="citation_date" content="2011/01/28" /><meta name="citation_author" content="Tom Madden" /><meta name="citation_fulltext_html_url" content="https://www.ncbi.nlm.nih.gov/books/NBK52636/" /><link rel="schema.DC" href="http://purl.org/DC/elements/1.0/" /><meta name="DC.Title" content="BLAST Help Manual Overview" /><meta name="DC.Type" content="Text" /><meta name="DC.Publisher" content="National Center for Biotechnology Information (US)" /><meta name="DC.Contributor" content="Tom Madden" /><meta name="DC.Date" content="2011/01/28" /><meta name="DC.Identifier" content="https://www.ncbi.nlm.nih.gov/books/NBK52636/" /><meta name="description" content="The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s. The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as a network service. The NCBI also distributes stand-alone BLAST applications for users who wish to run BLAST on their own machines or with their own databases. This document describes the stand-alone BLAST applications and will concentrate on the latest generation of such applications included in the BLAST+ package." /><meta name="og:title" content="BLAST Help Manual Overview" /><meta name="og:type" content="book" /><meta name="og:description" content="The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s. The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as a network service. The NCBI also distributes stand-alone BLAST applications for users who wish to run BLAST on their own machines or with their own databases. This document describes the stand-alone BLAST applications and will concentrate on the latest generation of such applications included in the BLAST+ package." /><meta name="og:url" content="https://www.ncbi.nlm.nih.gov/books/NBK52636/" /><meta name="og:site_name" content="NCBI Bookshelf" /><meta name="og:image" content="https://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-helpblast-lrg.png" /><meta name="twitter:card" content="summary" /><meta name="twitter:site" content="@ncbibooks" /><meta name="bk-non-canon-loc" content="/books/n/helpblast/introduction/" /><link rel="canonical" href="https://www.ncbi.nlm.nih.gov/books/NBK52636/" /><link rel="stylesheet" href="/corehtml/pmc/css/figpopup.css" type="text/css" media="screen" /><link rel="stylesheet" href="/corehtml/pmc/css/bookshelf/2.26/css/books.min.css" type="text/css" /><link rel="stylesheet" href="/corehtml/pmc/css/bookshelf/2.26/css/books_print.min.css" type="text/css" /><style type="text/css">p a.figpopup{display:inline !important} .bk_tt {font-family: monospace} .first-line-outdent .bk_ref {display: inline} </style><script type="text/javascript" src="/corehtml/pmc/js/jquery.hoverIntent.min.js"> </script><script type="text/javascript" src="/corehtml/pmc/js/common.min.js?_=3.18"> </script><script type="text/javascript">window.name="mainwindow";</script><script type="text/javascript" src="/corehtml/pmc/js/bookshelf/2.26/book-toc.min.js"> </script><script type="text/javascript" src="/corehtml/pmc/js/bookshelf/2.26/books.min.js"> </script>
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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>BLAST® Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2008-. </p></div></div></div>
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<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK52636_"><span class="title" itemprop="name">BLAST Help Manual Overview</span></h1><div class="contrib half_rhythm"><span itemprop="author">Tom Madden</span><div class="affiliation"><span class="email-label">Email: </span><a href="mailto:dev@null" data-email="vog.hin.mln.ibcn@neddam" class="oemail">vog.hin.mln.ibcn@neddam</a></div></div><p class="small">Created: <span itemprop="datePublished">January 28, 2011</span>.</p><p><em>Estimated reading time: 1 minute</em></p></div><div class="body-content whole_rhythm" itemprop="text"><p>The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s. The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as a network service. The NCBI also distributes stand-alone BLAST applications for users who wish to run BLAST on their own machines or with their own databases. This document describes the stand-alone BLAST applications and will concentrate on the latest generation of such applications included in the BLAST+ package.</p><p>The first two sections of this document are “quick start” guides that address setting BLAST+ up under UNIX (including LINUX and MacOSX) and Windows. The third section is a more in-depth look at the BLAST+ applications. These documents are currently being revised and may change substantially in coming releases.</p><div id="bk_toc_contnr"></div></div></div>
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