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<script type="text/javascript" src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/jr.boots.min.js"> </script><title>BLAST FTP Site - BLAST® Help - NCBI Bookshelf</title>
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<meta name="citation_date" content="2020/08/30">
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<meta name="citation_author" content="Tao Tao">
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<meta name="citation_author" content="Tom Madden">
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<meta name="citation_author" content="Camacho Christiam">
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yet</button><a id="jr-fip-next" class="wsprkl btn" title="Jump to next match">▶</a></nav></nav></div><div id="jr-epub-interstitial" class="hidden"></div><div id="jr-content"><article data-type="main"><div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><div class="fm-sec"><h1 id="_NBK62345_"><span class="title" itemprop="name">BLAST FTP Site</span></h1><p class="contribs">Tao T, Madden T, Christiam C.</p><p class="fm-aai"><a href="#_NBK62345_pubdet_">Publication Details</a></p><p><em>Estimated reading time: 11 minutes</em></p></div></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><p>The NCBI FTP server contains a BLAST-specific directory (<a href="https://ftp.ncbi.nlm.nih.gov/blast/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://ftp.ncbi.nlm.nih.gov/blast/</a>). Through this directory, the standalone BLAST packages and a standard set of BLAST databases are available to the public for download through anonymous FTP. For faster download, the service is also available through the Aspera client for those users with the Aspera browser plug-in installed (<a href="https://www.ncbi.nlm.nih.gov/public/?blast/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://www.ncbi.nlm.nih.gov/public/?blast/</a>).</p><p>This document describes the subdirectories and file contents of the BLAST FTP directory. Technical details on how to use certain files, especially those under the db (database) subdirectory, are also provided.</p><div id="blast_ftp_site.Subdirectories_under_the"><h2 id="_blast_ftp_site_Subdirectories_under_the_">Subdirectories under the BLAST FTP directory</h2><p>There are several subdirectories under the BLAST FTP directory. Each stores a set of files with similar types of content. These subdirectories are summarized in <a href="/books/NBK62345/table/blast_ftp_site.T.file_content_of_subdire/?report=objectonly" target="object" rid-ob="figobblastftpsiteTfilecontentofsubdire">Table 1</a>.</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figblastftpsiteTfilecontentofsubdire"><a href="/books/NBK62345/table/blast_ftp_site.T.file_content_of_subdire/?report=objectonly" target="object" title="Table 1. " class="img_link icnblk_img" rid-ob="figobblastftpsiteTfilecontentofsubdire"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/table-icon.gif" alt="Table Icon" /></a><div class="icnblk_cntnt"><h4 id="blast_ftp_site.T.file_content_of_subdire"><a href="/books/NBK62345/table/blast_ftp_site.T.file_content_of_subdire/?report=objectonly" target="object" rid-ob="figobblastftpsiteTfilecontentofsubdire">Table 1. </a></h4><p class="float-caption no_bottom_margin">File content of subdirectories under the "/blast" FTP directory </p></div></div></div><div id="blast_ftp_site.The_db_subdirectory"><h2 id="_blast_ftp_site_The_db_subdirectory_">The "<i>/db</i>" subdirectory</h2><p>This subdirectory contains a common set of preformatted BLAST database files in version 5 format. The FASTA sequences for a few widely used databases are stored under the "/FASTA" subdirectory. The contents of available preformatted databases are summarized separately according to their sequence nature and sources (for nucleotide databases). The databases provided for the cloud-based BLAST packages are under the "/cloud" subdirectory. The version 4 databases are kept in the "/v4" subdirectory, those entries will not be updated. The "/v5" subdirectory is a soft link back to the "/db" directory.</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figblastftpsiteTpreformattedproteinda"><a href="/books/NBK62345/table/blast_ftp_site.T.preformatted_protein_da/?report=objectonly" target="object" title="Table 2a. " class="img_link icnblk_img" rid-ob="figobblastftpsiteTpreformattedproteinda"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/table-icon.gif" alt="Table Icon" /></a><div class="icnblk_cntnt"><h4 id="blast_ftp_site.T.preformatted_protein_da"><a href="/books/NBK62345/table/blast_ftp_site.T.preformatted_protein_da/?report=objectonly" target="object" rid-ob="figobblastftpsiteTpreformattedproteinda">Table 2a. </a></h4><p class="float-caption no_bottom_margin">Preformatted protein database files </p></div></div><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figblastftpsiteTpreformattedrefseqnuc"><a href="/books/NBK62345/table/blast_ftp_site.T.preformatted_refseq_nuc/?report=objectonly" target="object" title="Table 2b. " class="img_link icnblk_img" rid-ob="figobblastftpsiteTpreformattedrefseqnuc"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/table-icon.gif" alt="Table Icon" /></a><div class="icnblk_cntnt"><h4 id="blast_ftp_site.T.preformatted_refseq_nuc"><a href="/books/NBK62345/table/blast_ftp_site.T.preformatted_refseq_nuc/?report=objectonly" target="object" rid-ob="figobblastftpsiteTpreformattedrefseqnuc">Table 2b. </a></h4><p class="float-caption no_bottom_margin">Preformatted RefSeq nucleotide database files </p></div></div><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figblastftpsiteTpreformattednonrefseq"><a href="/books/NBK62345/table/blast_ftp_site.T.preformatted_nonrefseq/?report=objectonly" target="object" title="Table 2c. " class="img_link icnblk_img" rid-ob="figobblastftpsiteTpreformattednonrefseq"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/table-icon.gif" alt="Table Icon" /></a><div class="icnblk_cntnt"><h4 id="blast_ftp_site.T.preformatted_nonrefseq"><a href="/books/NBK62345/table/blast_ftp_site.T.preformatted_nonrefseq/?report=objectonly" target="object" rid-ob="figobblastftpsiteTpreformattednonrefseq">Table 2c. </a></h4><p class="float-caption no_bottom_margin">Preformatted non-RefSeq nucleotide and target loci databases </p></div></div><div id="blast_ftp_site.Getting_the_preformatted"><h3>Getting the preformatted database files</h3><p>Preformatted BLAST database files offer several advantages over the FASTA files:</p><ul><li class="half_rhythm"><div>The preformatted databases are broken into smaller volumes and therefore can be downloaded more readily with fewer errors</div></li><li class="half_rhythm"><div>A convenient Perl script (<b><i>update_blastdb.pl</i></b> found in the bin directory of a locally installed blast+ package) is available to simplify the download of these preformatted databases</div></li><li class="half_rhythm"><div>Preformatted database files remove the makeblastdb formatting steps, and saves valuable processing time and diskspace</div></li><li class="half_rhythm"><div>Taxonomic information is encoded within the preformatted databases and can be used to limit the scope of a blast search, and sequence retrieval, and scientific name addition through the included taxdb files</div></li><li class="half_rhythm"><div>Sequences in FASTA format can be generated easily from the preformatted databases using the blastdbcmd utility when needed</div></li></ul><p>Preformatted databases must be downloaded in binary mode, downloading through the <i>update_blastdb.pl</i> script is recommeded. An example command line for getting the preformatted refseq_rna nucleotide database and the session output are given below.</p><pre>$ perl ../bin/blast+/update_blastdb.pl --passive --decompress refseq_rna<br />Connected to NCBI<br />Downloading refseq_rna (7 volumes) ...<br />Downloading refseq_rna.00.tar.gz... [OK]<br />Downloading refseq_rna.01.tar.gz... [OK]<br />Downloading refseq_rna.02.tar.gz... [OK]<br />Downloading refseq_rna.03.tar.gz... [OK]<br />Downloading refseq_rna.04.tar.gz... [OK]<br />Downloading refseq_rna.05.tar.gz... [OK]<br />Downloading refseq_rna.06.tar.gz... [OK]<br />Decompressing refseq_rna.00.tar.gz ... [OK]<br />Decompressing refseq_rna.01.tar.gz ... [OK]<br />Decompressing refseq_rna.02.tar.gz ... [OK]<br />Decompressing refseq_rna.03.tar.gz ... [OK]<br />Decompressing refseq_rna.04.tar.gz ... [OK]<br />Decompressing refseq_rna.05.tar.gz ... [OK]<br />Decompressing refseq_rna.06.tar.gz ... [OK]</pre><p>The complete options of this script (obtained using specific option "--help") are shown below.</p><pre>$ perl update_blastdb.pl --help<br />NAME<br /> update_blastdb.pl - Download pre-formatted BLAST databases<br /><br />SYNOPSIS<br /> update_blastdb.pl [options] blastdb ...<br /><br />OPTIONS<br /> --decompress<br /> Downloads, decompresses the archives in the current working directory,<br /> and deletes the downloaded archive to save disk space, while<br /> preserving the archive checksum files (default: false).<br /><br /> --showall<br /> Show all available pre-formatted BLAST databases (default: false). The<br /> output of this option lists the database names which should be used<br /> when requesting downloads or updates using this script.<br /><br /> It accepts the optional arguments: 'tsv' and 'pretty' to produce<br /> tab-separated values and a human-readable format respectively. These<br /> parameters elicit the display of additional metadata if this is<br /> available to the program. This metadata is displayed in columnar<br /> format; the columns represent:<br /><br /> name, description, size in gigabytes, date of last update (YYYY-MM-DD<br /> format).<br /><br /> --blastdb_version<br /> Specify which BLAST database version to download (default: 4).<br /> Supported values: 4, 5<br /><br /> --passive<br /> Use passive FTP, useful when behind a firewall or working in the cloud<br /> (default: true). To disable passive FTP, configure this option as<br /> follows: --passive no<br /><br /> --timeout<br /> Timeout on connection to NCBI (default: 120 seconds).<br /><br /> --force<br /> Force download even if there is a archive already on local directory<br /> (default: false).<br /><br /> --verbose<br /> Increment verbosity level (default: 1). Repeat this option multiple<br /> times to increase the verbosity level (maximum 2).<br /><br /> --quiet<br /> Produce no output (default: false). Overrides the --verbose option.<br /><br /> --version<br /> Prints this script's version. Overrides all other options.<br /><br /> --num_cores<br /> Sets the number of cores to utilize to perform downloads in parallel<br /> when data comes from GCS. Defaults to all cores (Linux and macos<br /> only).<br /><br />DESCRIPTION<br /> This script will download the pre-formatted BLAST databases requested in<br /> the command line from the NCBI ftp site.<br /><br />EXIT CODES<br /> This script returns 0 on successful operations that result in no<br /> downloads, 1 on successful operations that downloaded files, and 2 on<br /> errors.<br /><br />BUGS<br /> Please report them to <blast-help@ncbi.nlm.nih.gov><br /><br />COPYRIGHT<br /> See PUBLIC DOMAIN NOTICE included at the top of this script.</pre></div><div id="blast_ftp_site.Using_the_preformatted_BL"><h3>Using the preformatted BLAST database files</h3><p>The <i>--decompress</i> option of <i>updated_blastdb.pl</i> automatically decompresses and extract the archives of the requested database files. When manually downloading preformatted databases, those compressed archives must be downloaded in binary format using the passive mode, then inflated with <b><i>gunzip</i></b> or other decompress utilities. The working database files can then be extracted out of the resulting tar archive using <i>tar</i> program in Unix/Linux or <i>WinZip</i> and <i>StuffIt Expander</i> on Windows and Macintosh platforms, respectively.</p><p>Large databases are formatted in multiple gigbytes-sized volumes, which are named using the "name.##.tar.gz" convention. To reconstitute a given multi-volume database, all volumes with the same base database name are required. A database alias file, with ".pal" extension for protein or ".nal" extension for nucleotide, is provided to tie the volumes together. The database can be called using the base database name. For example, binary programs from the blast+ package can call the nt database using the command line option of "<b>-db nt</b>" option argument.</p><p>For proper setup of standalone blast+, it is recommended that database files be stored in a centralized directory, with the path to this directory be encoded by the BLASTDB variable. Details are available in the setup document for <a href="/books/n/helpblast/blast_setup_pc/?report=reader">Windows</a> and <a href="/books/n/helpblast/chapter1/?report=reader">Mac/Linux/Unix</a>.</p></div><div id="blast_ftp_site.Sequence_files_under_the"><h3>Sequence files under the "/db/FASTA/" subdirectory</h3><p>This subdirectory contains sequence files in the FASTA format. With preformatted databases readily available, only a few commonly used databases are available in this format.</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figblastftpsiteTproteindatabasefiles"><a href="/books/NBK62345/table/blast_ftp_site.T.protein_database_files/?report=objectonly" target="object" title="Table 3. " class="img_link icnblk_img" rid-ob="figobblastftpsiteTproteindatabasefiles"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/table-icon.gif" alt="Table Icon" /></a><div class="icnblk_cntnt"><h4 id="blast_ftp_site.T.protein_database_files"><a href="/books/NBK62345/table/blast_ftp_site.T.protein_database_files/?report=objectonly" target="object" rid-ob="figobblastftpsiteTproteindatabasefiles">Table 3. </a></h4><p class="float-caption no_bottom_margin">Protein database files under the /db/FASTA directory </p></div></div><p>For local BLAST searches, the recommendation is to use the preformatted version given in the parent directory. For those without preformatted counterparts, the FASTA sequence file first need to be inflated using gunzip or other comparable utilities, the resulting file can then be formatted by <i>makeblastdb</i> from the blast+ package. Example command lines for formatting igSeqNt and igSeqProt are given below.</p><pre>$ makeblastdb –in swissprot –dbtype prot –parse_seqids <br />$ makeblastdb –in nt –dbtype nucl –parse_seqids </pre><p>For vector screening needs, get the FASTA sequences from this ftp directory and formatted them using makeblastdb:</p><pre><a href="https://ftp.ncbi.nlm.nih.gov/pub/UniVec/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://ftp.ncbi.nlm.nih.gov/pub/UniVec/</a> </pre><p>Chromosome entries are available in the refseq_euk_rep_genomes and refseq_prok_rep_genomes databases. Organism-specific sequences are available in FASTA format under the genomes FTP directory:</p><pre><a href="https://ftp.ncbi.nlm.nih.gov/pub/genomes/all/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://ftp.ncbi.nlm.nih.gov/pub/genomes/all/</a> <a href="https://ftp.ncbi.nlm.nih.gov/pub/factsheets/Factsheet_Assembly.pdf" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://ftp.ncbi.nlm.nih.gov/pub/factsheets/Factsheet_Assembly.pdf</a> </pre><p>The NCBI Datasets tool is another way to get the genomic data from NCBI. Please refer to this page for more information: <a href="https://www.ncbi.nlm.nih.gov/datasets" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://www.ncbi.nlm.nih.gov/datasets</a></p></div><div id="blast_ftp_site.Database_files_under_the"><h3>Database files under the "/db/v4/" subdirectory</h3><p>This subdirectory contains the preformatted blast dtabase files in the older version 4 format. Those databases will not be updated. They are meant as a stop-gap measure to ease the transition to version 5 of the databases. Content description for this subdirectory will be skipped.</p></div><div id="blast_ftp_site.Database_update"><h3>Database update</h3><p>In general, BLAST databases are updated daily. There is no established incremental update scheme due to sequence removal and update. It is recommended that databases be downloaded at regular intervals to keep the content of local copy current. The <b><i>update_blastdb.pl</i></b> script can help streamline this download process. If the original database.##.tar.gz files are kept, this utility can automatically check the time stamps to determine if file refreshing is required or not.</p><p>Faster download through Aspera plug-in is also possible (downloadable from the <a href="http://www.asperasoft.com/en/documentation/8" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Aspera Soft site</a> under the download tab). A web interface for the NCBI FTP site is at: <a href="https://www.ncbi.nlm.nih.gov/public/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://www.ncbi.nlm.nih.gov/public/</a>. Aspera’s commandline client ascp can be used to access Aspera indexed NCBI ftp site.</p></div></div><div id="blast_ftp_site.Contents_of_the_blastdemo"><h2 id="_blast_ftp_site_Contents_of_the_blastdemo_">Contents of the "/blast/demo/" subdirectory</h2><p>This directory contains technical presentations given by NCBI BLAST developers in scientific conferences and several tools and documents relevant to the BLAST service to deomonstrate how specific functions from NCBI's C-toolkit code can be used.</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figblastftpsiteTcontentsoftheblastde"><a href="/books/NBK62345/table/blast_ftp_site.T.contents_of_the_blastde/?report=objectonly" target="object" title="Table 4. " class="img_link icnblk_img" rid-ob="figobblastftpsiteTcontentsoftheblastde"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/table-icon.gif" alt="Table Icon" /></a><div class="icnblk_cntnt"><h4 id="blast_ftp_site.T.contents_of_the_blastde"><a href="/books/NBK62345/table/blast_ftp_site.T.contents_of_the_blastde/?report=objectonly" target="object" rid-ob="figobblastftpsiteTcontentsoftheblastde">Table 4. </a></h4><p class="float-caption no_bottom_margin">Contents of the /blast/demo/ subdirectory </p></div></div><p>Since NCBI is migrating to C++ code base provided by the <a href="ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">C++ toolkit</a>, some of the files from this directory could become obsolete or change without notice. Most of the functions demonstrated here are incorporated in the <i>blast_formatter</i> utility distributed in the <a href="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">blast+ package</a>.</p></div><div id="blast_ftp_site.Contents_of_the_blastdocu"><h2 id="_blast_ftp_site_Contents_of_the_blastdocu_">Contents of the "/blast/documents/" subdirectory</h2><p>This directory contains mostly posters and other preliminary documentation from BLAST developers. For blast+ packages, a <a href="/books/n/helpblastclaum/?report=reader">user manual</a> along with the <a href="/books/n/helpblast/?report=reader">instruction for installation</a> are available through <a href="/books/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCBI bookshelf</a>. Content description will be skipped. See the README for this directory for details: <a href="https://ftp.ncbi.nlm.nih.gov/blast/documents/README" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://ftp.ncbi.nlm.nih.gov/blast/documents/README</a></p></div><div id="blast_ftp_site.Contents_of_the_blastexec"><h2 id="_blast_ftp_site_Contents_of_the_blastexec_">Contents of the "/blast/executables/" subdirectory</h2><p>This directory contains several subdirectories each for a set of BLAST distribution packages from a specific release. Binaries based on the new C++ toolkit are under the /blast+ subdirectory with the lastest release directly accessible through the /LATEST symbolic link. The only program file is <b>remote_fuser</b>, for use in database fetching in the cloud implementation.</p><div id="blast_ftp_site.Contents_of_the_blastexec_1"><h3>Contents of the "/blast/executables/LATEST/" subdirectory</h3><p>This directory is a symbolic link pointing to the LATEST release of BLAST+ programs built from the NCBI C++ toolkit. Packages for commom platforms available in different formats are summarized in <a href="/books/NBK62345/table/blast_ftp_site.T.file_content_of_the_bla/?report=objectonly" target="object" rid-ob="figobblastftpsiteTfilecontentofthebla">Table 5</a> below.</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figblastftpsiteTfilecontentofthebla"><a href="/books/NBK62345/table/blast_ftp_site.T.file_content_of_the_bla/?report=objectonly" target="object" title="Table 5. " class="img_link icnblk_img" rid-ob="figobblastftpsiteTfilecontentofthebla"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/table-icon.gif" alt="Table Icon" /></a><div class="icnblk_cntnt"><h4 id="blast_ftp_site.T.file_content_of_the_bla"><a href="/books/NBK62345/table/blast_ftp_site.T.file_content_of_the_bla/?report=objectonly" target="object" rid-ob="figobblastftpsiteTfilecontentofthebla">Table 5. </a></h4><p class="float-caption no_bottom_margin">File content of the /blast/executables/LATEST/ subdirectory </p></div></div><p>All non-source code archives or packages are equivalent. They contain a standard collection of standalone command line programs and accessory utilities for different platforms. Installation of the package enables local BLAST searches, custom database preparation from FASTA sequences, as well as sequence retrieval from existing databases formatted with the "-parse_seqids" argument.</p><p>Details on individual programs from the package as well as installation procedures are available for <a href="/books/n/helpblast/blast_setup_pc/?report=reader#blast_setup_pc.Installation">Windows</a> and <a href="/books/n/helpblast/chapter1/?report=reader#chapter1.Installation">Mac/Linux/Unix</a>.</p><p>Note that blast+ does not provide a separate client-server tool. That function is built into individual blast programs, i.e. <i>blastn</i>, <i>blastp</i>, <i>blastx</i>, <i>tblastn</i> and <i>tblastx</i>, and can be invoked using the "-remote" option. The "-remote" option enables remote search against databases at NCBI using NCBI’s computation resources. In addition, blast+ does not provide package equivalent to the decommissioned wwwblast package.</p></div><div id="blast_ftp_site.Contents_of_the_blastexec_2"><h3>Contents of the "/blast/executables/blast+/" subdirectory</h3><p>This subdirectory archives all releases of the blast+ package. Each release is under its own directory named using its version number. Available builds start at version 2.2.18, with verision 2.2.20 skipped. Optional version 5 database support began in release 2.8.0alpha.</p></div><div id="blast_ftp_site.Contents_of_the_blastexec_3"><h3>Contents of the "/blast/executables/legacy.NOTSUPPORTED/" subdirectory</h3><p>This subdirectory archives the releases of legacy blast package based on the NCBI C Toolkit. They are meant for historical references, NCBI no longer supports them. Each release is under its own directory with the version number as its name. Available builds start at version 2.0.7.</p><p>Packages with version number 2.2.10 or newer are packaged with a built-in directory structure to better organize the distributed contents.</p></div><div id="blast_ftp_site.Contents_of_the_blastexec_4"><h3>Contents of the "/blast/executables/igblast/" subdirectory</h3><p>This subdirectory archives the different releases of standalone igblat package (under the release subdirectory. The separate data files and database files required by the binary programs in this package are available in subdirectories separate from each releases.</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figblastftpsiteTfilecontentofthebla1"><a href="/books/NBK62345/table/blast_ftp_site.T.file_content_of_the_bla_1/?report=objectonly" target="object" title="Table 6. " class="img_link icnblk_img" rid-ob="figobblastftpsiteTfilecontentofthebla1"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/table-icon.gif" alt="Table Icon" /></a><div class="icnblk_cntnt"><h4 id="blast_ftp_site.T.file_content_of_the_bla_1"><a href="/books/NBK62345/table/blast_ftp_site.T.file_content_of_the_bla_1/?report=objectonly" target="object" rid-ob="figobblastftpsiteTfilecontentofthebla1">Table 6. </a></h4><p class="float-caption no_bottom_margin">File content of the /blast/executables/igblast/release/ subdirectory </p></div></div></div><div id="blast_ftp_site.Contents_of_the_blastexec_5"><h3>Contents of the "/blast/executables/magicblast/" subdirectory</h3><p>A subdirectory for the releases of a next generation sequence read mapper from NCBI. The LATEST directory maps to the current release’s directory. Refer to the README file under the subdirectory for more details. Details technical description of the package is at: <a href="https://ncbi.github.io/magicblast/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://ncbi.github.io/magicblast/</a>.</p></div><div id="blast_ftp_site.Contents_of_the_blastexec_6"><h3>Contents of the "/blast/executables/rmblast/" subdirectory</h3><p>This subdirectory archives the repeat masker BLAST. Only two releases, 2.2.27 and 2.2.28, are available. Refer to the readme for more details.</p></div></div><div id="blast_ftp_site.Contents_of_the_blastmatr"><h2 id="_blast_ftp_site_Contents_of_the_blastmatr_">Contents of the "/blast/matrices/" subdirectory</h2><p>This directory contains an extensive list of score matrices, most of which are experimental in nature and not supported by blast programs. The matrices can be grouped into PAM family of matrices, BLOSUM family of matrices, matrices for nucleotide and other miscellaneous matrices.</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figblastftpsiteTsummaryofmatricesfou"><a href="/books/NBK62345/table/blast_ftp_site.T.summary_of_matrices_fou/?report=objectonly" target="object" title="Table 7. " class="img_link icnblk_img" rid-ob="figobblastftpsiteTsummaryofmatricesfou"><img class="small-thumb" src="/corehtml/pmc/css/bookshelf/2.26/img/table-icon.gif" alt="Table Icon" /></a><div class="icnblk_cntnt"><h4 id="blast_ftp_site.T.summary_of_matrices_fou"><a href="/books/NBK62345/table/blast_ftp_site.T.summary_of_matrices_fou/?report=objectonly" target="object" rid-ob="figobblastftpsiteTsummaryofmatricesfou">Table 7. </a></h4><p class="float-caption no_bottom_margin">Summary of matrices found in the /blast/matrices/ subdirectory </p></div></div></div><div id="blast_ftp_site.Contents_of_the_blasttemp"><h2 id="_blast_ftp_site_Contents_of_the_blasttemp_">Contents of the "/blast/temp/" subdirectory</h2><p>This is a directory used for testing purposes or other special needs that do not fall into the above categories.</p></div><div id="blast_ftp_site.Contents_of_the_blastWGS"><h2 id="_blast_ftp_site_Contents_of_the_blastWGS_">Contents of the "/blast/WGS_TOOLS/" subdirectory</h2><p>This directory provides two database alias generating tools for WGS and TSA datasets, respectively. These tools take an input taxonomic id and generate a database alias for project-based WGS or TSA datasets - those with four letter project prefix as listed at <a href="https://www.ncbi.nlm.nih.gov/Traces/wgs/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://www.ncbi.nlm.nih.gov/Traces/wgs/</a>. The alias file produced can be used with the vdb blast tools available from the sratoolkit, which is available for common platforms: <a href="https://www.ncbi.nlm.nih.gov/Traces/sra/?view=software" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://www.ncbi.nlm.nih.gov/Traces/sra/?view=software</a>. A handout describing the general usage of these vdb blast programs is available at:</p><p>
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<a href="ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_Local_SRA_BLAST.pdf" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_Local_SRA_BLAST.pdf</a>
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</p></div><div id="blast_ftp_site.Getting_Help"><h2 id="_blast_ftp_site_Getting_Help_">Getting Help</h2><p>For details, please refer to documents under the <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Help tab</a> of the BLAST homepage or the <a href="ftp://ftp.ncbi.nlm.nih.gov/blast/documents/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=ftp">document directory</a> under the BLAST FTP site.</p><p>Comments, questions and bug reports specifically relating to the BLAST programs and their usage should be sent to <a href="mailto:dev@null" data-email="vog.hin.mln.ibcn@pleh-tsalb" class="oemail">vog.hin.mln.ibcn@pleh-tsalb</a>.</p></div><div id="bk_toc_contnr"></div></div></div><div class="fm-sec"><h2 id="_NBK62345_pubdet_">Publication Details</h2><h3>Author Information and Affiliations</h3><div class="contrib half_rhythm"><span itemprop="author">Tao Tao</span>, PhD<div class="affiliation small">NCBI<div><span class="email-label">Email: </span><a href="mailto:dev@null" data-email="vog.hin.mln.ibcn@oat" class="oemail">vog.hin.mln.ibcn@oat</a></div></div><div class="small">Corresponding author.</div></div><div class="contrib half_rhythm"><span itemprop="author">Tom Madden</span>, PhD<div class="affiliation small">NCBI<div><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></div><div class="contrib half_rhythm"><span itemprop="author">Camacho Christiam</span><div class="affiliation small">NCBI<div><span class="email-label">Email: </span><a href="mailto:dev@null" data-email="vog.hin.mln.ibcn@ohcamac" class="oemail">vog.hin.mln.ibcn@ohcamac</a></div></div></div><h3>Publication History</h3><p class="small">Created: <span itemprop="datePublished">May 29, 2011</span>; Last Update: <span itemprop="dateModified">August 30, 2020</span>.</p><h3>Copyright</h3><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a><p class="small">BLAST is a Registered Trademark of the National Library of Medicine</p></div></div><h3>Publisher</h3><p><a href="http://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>, Bethesda (MD)</p><h3>NLM Citation</h3><p>Tao T, Madden T, Christiam C. BLAST FTP Site. 2011 May 29 [Updated 2020 Aug 30]. In: BLAST® Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2008-. <span class="bk_cite_avail"></span></p></div><div class="small-screen-prev"><a href="/books/n/helpblast/Blast_ReleaseNotes/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M75,30 c-80,60 -80,0 0,60 c-30,-60 -30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Prev</text></svg></a></div><div class="small-screen-next"><a href="/books/n/helpblast/blast_glossary/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M25,30c80,60 80,0 0,60 c30,-60 30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Next</text></svg></a></div></article><article data-type="table-wrap" id="figobblastftpsiteTfilecontentofsubdire"><div id="blast_ftp_site.T.file_content_of_subdire" class="table"><h3><span class="label">Table 1. </span></h3><div class="caption"><p>File content of subdirectories under the "/blast" FTP directory</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK62345/table/blast_ftp_site.T.file_content_of_subdire/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__blast_ftp_site.T.file_content_of_subdire_lrgtbl__"><table><thead><tr><th id="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Subdirectory</th><th id="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">File content</th></tr></thead><tbody><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">db</td><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Preformatted BLAST database files and FASTA sequence files (only for a few representative databases, kept under the /FASTA subdirectory)</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">
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<a href="#blast_ftp_site.Contents_of_the_blastdemo">demo</a>
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</td><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Various demonstration packages for software developers</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">
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<a href="#blast_ftp_site.Contents_of_the_blastdocu">documents</a>
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</td><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Preliminary documentation (mostly from software developers) and pointers to other documentation</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">
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<a href="#blast_ftp_site.Contents_of_the_blastexec">executables</a>
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</td><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Different releases for standalone BLAST packages, including blast+</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">
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<a href="#blast_ftp_site.Contents_of_the_blastmatr">matrices</a>
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</td><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Different scoring matrices, only a selected subset are supported by blast</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">
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<a href="#blast_ftp_site.Contents_of_the_blasttemp">temp</a>
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</td><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Miscellaneous files</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">
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<a href="#blast_ftp_site.Contents_of_the_blastWGS">WGS_TOOLS</a>
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</td><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Perl scripts for generating WGS project-based database alias for TSA and WGS datasets, to be used with vdb blast</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">windowmasker_files</td><td headers="hd_h_blast_ftp_site.T.file_content_of_subdire_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">A collection of windowmasker files, organized into subdirectory named by the taxonomic ids</td></tr></tbody></table></div></div></article><article data-type="table-wrap" id="figobblastftpsiteTpreformattedproteinda"><div id="blast_ftp_site.T.preformatted_protein_da" class="table"><h3><span class="label">Table 2a. </span></h3><div class="caption"><p>Preformatted protein database files</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK62345/table/blast_ftp_site.T.preformatted_protein_da/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__blast_ftp_site.T.preformatted_protein_da_lrgtbl__"><table><thead><tr><th id="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">File name</th><th id="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Contents</th></tr></thead><tbody><tr><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">landmark.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">The landmark database includes complete proteomes from a few selected representative genomes spanning a wide taxonomic range, the main database used by the SmartBLAST services.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">cdd_delta.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Condensed conserved domain database for use with deltablast protein searches.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">nr.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">A collection of protein sequences with entries from GenPept, Swissprot, PDB, PRF, PIR and NCBI Reference Sequence (RefSeq) project.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">pataa.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Protein sequences from patents as supplied by USPTO. These entries are EXCLUDED from the nr database.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">pdbaa.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Protein sequences from PDB structure records’ protein components.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">refseq_protein.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Protein sequences from NCBI RefSeq project.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">swissprot.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Protein sequences from the swiss-prot sequence database (last major update).</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">tsa_nr.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Protein sequences from the Trascriptome Shotgun Assembly. Its entries are EXCLUDED from the nr database.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">env_nr.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_protein_da_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Protein sequences from large environmental sequencing projects, e.g., Sargasso Sea, Acid Mine Drainage. Its entries are EXCLUDED from the nr database.</td></tr></tbody></table></div></div></article><article data-type="table-wrap" id="figobblastftpsiteTpreformattedrefseqnuc"><div id="blast_ftp_site.T.preformatted_refseq_nuc" class="table"><h3><span class="label">Table 2b. </span></h3><div class="caption"><p>Preformatted RefSeq nucleotide database files</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK62345/table/blast_ftp_site.T.preformatted_refseq_nuc/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__blast_ftp_site.T.preformatted_refseq_nuc_lrgtbl__"><table><thead><tr><th id="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">File</th><th id="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Contents</th></tr></thead><tbody><tr><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">16S_ribosomal_RNA.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Microbial 16S RNA sequences from the RefSeq Targeted Loci project (<a href="https://www.ncbi.nlm.nih.gov/refseq/targetedloci/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">https://www<wbr style="display:inline-block"></wbr>​.ncbi.nlm<wbr style="display:inline-block"></wbr>​.nih.gov/refseq/targetedloci/</a>).</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">refseq_rna.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">RNA sequences from NCBI RefSeq project, also included in the nt database.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">refseq_euk_rep_genomes.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Eukaryotic representative genomes from NCBI RefSeq project</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">refseq_prok_rep_genomes.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Prokaryotic representative genomes from NCBI RefSeq project</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">refseq_viroids_rep_genomes.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Viriods representative genomes from NCBI RefSeq project</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">refseq_viruses_rep_genomes.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Viruses representative genomes from NCBI RefSeq project</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">human_genome.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Current refseq human genome assembly (GRCh) with various database masking</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">mouse_genome.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_refseq_nuc_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Current refseq mouse genome assembly (GRCm) with various database masking</td></tr></tbody></table></div></div></article><article data-type="table-wrap" id="figobblastftpsiteTpreformattednonrefseq"><div id="blast_ftp_site.T.preformatted_nonrefseq" class="table"><h3><span class="label">Table 2c. </span></h3><div class="caption"><p>Preformatted non-RefSeq nucleotide and target loci databases</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK62345/table/blast_ftp_site.T.preformatted_nonrefseq/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__blast_ftp_site.T.preformatted_nonrefseq_lrgtbl__"><table><thead><tr><th id="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">File</th><th id="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Contents</th></tr></thead><tbody><tr><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">nt.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">The nucleotide sequence database contains entries from traditional divisions of GenBank, EMBL and DDBJ. Sequences from bulk divisions, i.e., gss, sts, pat, est, htg, wgs, con, and environmental sequences are excluded. RefSeq genomic entries are also excluded.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">patnt.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Nucleotide sequences from patents as supplied by USPTO to GenBank, or from EU/Japan Patent Agencies through EMBL/DDBJ. Entries are <b>EXCLUDED</b> from the nt database.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">pdbnt.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Sequences for the nucleotide components of PDB structure records.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">tsa_nt.##.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">A database with earlier non-project based Transcriptome Shotgun Assembly (TSA) entries. Project-based TSA entries are NOT included. Entries are <b>EXCLUDED</b> from the nt database.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">ITS_*.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Databases with collection fungal or eukaryotic Internal Transcribed Spacer sequences.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">LSU_*_rRNA.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Database with large submit rRNA sequences for prokaryotes and eukaryotes.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">SSU_*_rRNA.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">A database with sequences small from fungi and eukaryotes</td></tr><tr><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">taxdb.tar.gz</td><td headers="hd_h_blast_ftp_site.T.preformatted_nonrefseq_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">A non-sequence database file containing taxonomic information for sequences in the preformatted databases providing common and scientific names for each entry.</td></tr></tbody></table></div></div></article><article data-type="table-wrap" id="figobblastftpsiteTproteindatabasefiles"><div id="blast_ftp_site.T.protein_database_files" class="table"><h3><span class="label">Table 3. </span></h3><div class="caption"><p>Protein database files under the /db/FASTA directory</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK62345/table/blast_ftp_site.T.protein_database_files/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__blast_ftp_site.T.protein_database_files_lrgtbl__"><table><thead><tr><th id="hd_h_blast_ftp_site.T.protein_database_files_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">File</th><th id="hd_h_blast_ftp_site.T.protein_database_files_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Content</th></tr></thead><tbody><tr><td headers="hd_h_blast_ftp_site.T.protein_database_files_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">nr.gz</td><td headers="hd_h_blast_ftp_site.T.protein_database_files_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">The FASTA equivalent of the nr.##.tar.gz database files</td></tr><tr><td headers="hd_h_blast_ftp_site.T.protein_database_files_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">swissprot.gz</td><td headers="hd_h_blast_ftp_site.T.protein_database_files_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">The FASTA equivalent of the swissprot.tar.gz database file.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.protein_database_files_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">nt.gz</td><td headers="hd_h_blast_ftp_site.T.protein_database_files_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">The FASTA equivalent of the nt.##.tar.gz database files.</td></tr></tbody></table></div></div></article><article data-type="table-wrap" id="figobblastftpsiteTcontentsoftheblastde"><div id="blast_ftp_site.T.contents_of_the_blastde" class="table"><h3><span class="label">Table 4. </span></h3><div class="caption"><p>Contents of the /blast/demo/ subdirectory</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK62345/table/blast_ftp_site.T.contents_of_the_blastde/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__blast_ftp_site.T.contents_of_the_blastde_lrgtbl__"><table><thead><tr><th id="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">File/Dir Name</th><th id="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Content</th></tr></thead><tbody><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">QUICKBLASTP</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Standalone kmer indexing tool and the kmer blastp tool. The algorithm is used by the web protein blast search when "Quick BLASTP (Accelerated protein-protein BLAST) " option is selected</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">README.quickblastp</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Readme for quickblastp</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">quickblastp.tar.gz</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Kmer-based quickblastp demonstration package</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">benchmark</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Package with sample database and query for gauging the performance of BLAST releases on different platforms</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">bmc</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Sequences used in the generation of BLAST search data for the blast+ paper published in BMC</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">igblast</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Directory with igblast related set of scripts, see its README for more details</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">magicbkast_article</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Supplemental materials for the magicblast paper and the binary used to generate the specs</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">blast_programming.ppt</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">PowerPoint presentation on BLAST programing</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">mt_tback.tgz</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Multi-threaded traceback related test code</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">openmp_test.tar.gz</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Openmp multi-thread related test code</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">parse_blast_xml.tar.gz</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Demo package on parsing xml styled blast output</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">test_suite.tar.gz</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">An old set of test sequences with csh script</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">vecscreen</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Binary program for vecscreen</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">*.ppt, *.pdf</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Slides or posters presented by the BLAST group in various conferences</td></tr><tr><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">*.fsa</td><td headers="hd_h_blast_ftp_site.T.contents_of_the_blastde_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Miscellaneous sequences</td></tr></tbody></table></div></div></article><article data-type="table-wrap" id="figobblastftpsiteTfilecontentofthebla"><div id="blast_ftp_site.T.file_content_of_the_bla" class="table"><h3><span class="label">Table 5. </span></h3><div class="caption"><p>File content of the /blast/executables/LATEST/ subdirectory</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK62345/table/blast_ftp_site.T.file_content_of_the_bla/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__blast_ftp_site.T.file_content_of_the_bla_lrgtbl__"><table><thead><tr><th id="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">File</th><th id="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Contents</th></tr></thead><tbody><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">ChangeLog</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Changes introduced in this release</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">ncbi-blast-*src.*</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">blast+ source code in different formats</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">ncbi-blast-#.#.##+.x86_64.rpm</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">rpm installation package for PC running 64-bit Linux</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">ncbi-blast-#.#.##+-x64-linux.tar.gz</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Tar archive for PC running 64-bit Linux</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">ncbi-blast-*.dmg</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Disk image for Macintosh running 64-bit OSX</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">ncbi-blast-*-macosx.tar.gz</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Tar archive for Macintosh running 64-bit OSX</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">ncbi-blast-*-win64.exe</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Installer for PC running 64-bit Windows</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">ncbi-blast-#.#.##+-x64-win64.tar.gz</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Tar archive for PC running 64-bit Windows</td></tr></tbody></table></div></div></article><article data-type="table-wrap" id="figobblastftpsiteTfilecontentofthebla1"><div id="blast_ftp_site.T.file_content_of_the_bla_1" class="table"><h3><span class="label">Table 6. </span></h3><div class="caption"><p>File content of the /blast/executables/igblast/release/ subdirectory</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK62345/table/blast_ftp_site.T.file_content_of_the_bla_1/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__blast_ftp_site.T.file_content_of_the_bla_1_lrgtbl__"><table class="no_bottom_margin"><thead><tr><th id="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">File</th><th id="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Contents</th></tr></thead><tbody><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">#.#.#</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Different release directories</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">LATEST</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Soft link pointing to the latest release subdirectory</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">database *</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">germline immunoglobulin gene sequences for mouse and rhesus monkey. Databases for other organisms are NOT provided due to license requirement.</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Internal_data</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Internal vdj gene information file for annotation need</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">optional_file</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Additional gene annotation file</td></tr><tr><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">edit_imgt_file.pl *</td><td headers="hd_h_blast_ftp_site.T.file_content_of_the_bla_1_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">A perl script for manipulating the deflines of IMGT immunoglobulin sequences so they can be used as input to make databases through makeblastdb</td></tr></tbody></table></div><div class="tblwrap-foot"><div><dl class="temp-labeled-list small"><dl class="bkr_refwrap"><dt>* </dt><dd><div id="blast_ftp_site.TF.6.1"><p class="no_margin">Note: Internal_data, optional_file, and database directories are included in release 1.13.0 or later; use the files downloaded wit hthe release. Additionally, license requirement prevents NCBI from distributing the germline sequences for certain organisms as blast-ready databases. Instead, those sequences should be obtained from IMGT as FASTA. Convert the deflines of the IMGT sequences using the "edit_imgt_file.pl" script first before using makeblastdb to format the file into a igblast readable database.</p></div></dd></dl></dl></div></div></div></article><article data-type="table-wrap" id="figobblastftpsiteTsummaryofmatricesfou"><div id="blast_ftp_site.T.summary_of_matrices_fou" class="table"><h3><span class="label">Table 7. </span></h3><div class="caption"><p>Summary of matrices found in the /blast/matrices/ subdirectory</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK62345/table/blast_ftp_site.T.summary_of_matrices_fou/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__blast_ftp_site.T.summary_of_matrices_fou_lrgtbl__"><table><thead><tr><th id="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">File</th><th id="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Contents</th></tr></thead><tbody><tr><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">BLOSUM*</td><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">BLOSUM family of score matrices for protein alignment</td></tr><tr><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">PAM*</td><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">PAM family of score matrices for protein alignment</td></tr><tr><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">DAYHOFF*, GONNET*</td><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Variants of PAM matrices for protein alignment</td></tr><tr><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">MATCH, IDENTITY</td><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Simplified score matrices for protein alignment</td></tr><tr><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">NUC*</td><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">Nucleotide score matrices</td></tr><tr><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">PAM.tar.gz</td><td headers="hd_h_blast_ftp_site.T.summary_of_matrices_fou_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">C source code for generating PAM matrices</td></tr></tbody></table></div></div></article></div><div id="jr-scripts"><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/libs.min.js"> </script><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/jr.min.js"> </script></div></div>
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