92 lines
50 KiB
HTML
92 lines
50 KiB
HTML
<!DOCTYPE html>
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/*# sourceURL=/css/ampshared.css*/</style><meta property="og:locale" content="en_US"><meta property="og:type" content="article"><meta property="og:title" content="BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024 - NCBI Insights"><meta property="og:description" content="Easily generate BLAST FASTA files yourself! In April 2024, the FASTA (sequence text) files of the sequences in the Basic Alignment Search Tool (BLAST) databases will no longer be available on the FTP site. However, you can easily generate FASTA files yourself from the formatted BLAST databases by using the BLAST utility blastdbcmd that comes … Continue reading BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024 →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/"><meta property="og:site_name" content="NCBI Insights"><meta property="article:publisher" content="https://www.facebook.com/ncbi.nlm"><meta property="article:published_time" content="2024-01-25T18:12:00+00:00"><meta name="author" content="NCBI Staff"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@NCBI"><meta name="twitter:site" content="@NCBI"><meta name="twitter:label1" content="Written by"><meta name="twitter:data1" content="NCBI Staff"><meta name="twitter:label2" content="Est. reading time"><meta name="twitter:data2" content="1 minute"><meta name="robots" content="index, follow, 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<h1 class="amp-wp-title">BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024</h1>
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<time datetime="2024-01-25T18:12:00+00:00">
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1 year ago </time>
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<h3><i><span data-contrast="auto">Easily generate BLAST FASTA files yourself!</span></i><span data-ccp-props='{"201341983":0,"335559739":160,"335559740":259}'> </span></h3>
|
||
<p><span data-contrast="auto">In April 2024, the FASTA (sequence text) files of the sequences in the </span><a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=blast-fasta-unavailable-20240125"><span data-contrast="none">Basic Alignment Search Tool (BLAST)</span></a><span data-contrast="auto"> databases will no longer be available on the <a href="https://ftp.ncbi.nlm.nih.gov/">FTP</a> site. However, you can easily generate FASTA files yourself from the formatted BLAST databases by using the BLAST utility blastdbcmd that comes with the standalone BLAST programs. This provides you the flexibility to generate organism-specific FASTA files using NCBI’s taxonomy IDs for specific organisms or groups. </span><span data-ccp-props='{"134233117":true,"134233118":true,"201341983":0,"335559739":160,"335559740":240}'> </span></p>
|
||
<p><span data-contrast="auto">See the examples below and the </span><a href="https://www.ncbi.nlm.nih.gov/books/NBK279690/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=blast-fasta-unavailable-20240125"><span data-contrast="auto">BLAST Command Line Applications User Manual</span></a><span data-contrast="auto"> for more details on the standalone BLAST programs and working with the BLAST databases.</span><span data-ccp-props='{"134233117":true,"134233118":true,"201341983":0,"335559739":160,"335559740":240}'> </span></p>
|
||
<h5 aria-level="2"><span data-contrast="none">Example command-lines</span><span data-ccp-props='{"134245418":true,"134245529":true,"201341983":0,"335559738":40,"335559739":0,"335559740":259}'> </span></h5>
|
||
<ul>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="3" data-list-defn-props='{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f">Generating FASTA file of the default nucleotide database </span></li>
|
||
</ul>
|
||
<pre>blastdbcmd -db nt -entry all -out nt.fsa<span data-ccp-props='{"134233117":true,"134233118":true,"201341983":0,"335559685":720,"335559739":160,"335559740":240}' data-amp-original-style="font-size: 1.125rem;" class="amp-wp-2917c00"> </span></pre>
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||
<ul>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="3" data-list-defn-props='{"335552541":1,"335559684":-2,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span data-contrast="auto" data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f">Generating FASTA file of primate (taxonomy ID 9443) sequences from the refseq_protein database</span></li>
|
||
</ul>
|
||
<pre><span data-amp-original-style="font-size: 15px;" class="amp-wp-499df8f">blastdbcmd -db refseq_protein -taxids 9443 -target_only -out refseq_prot.primates.fsa </span></pre>
|
||
<p><span data-contrast="auto">Note: Use </span><a href="https://www.ncbi.nlm.nih.gov/taxonomy/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=blast-fasta-unavailable-20240125"><span data-contrast="auto">NCBI Taxonomy</span></a><span data-contrast="auto"> to look up IDs for organisms or taxonomic groups.</span><span data-ccp-props='{"134233117":true,"134233118":true,"201341983":0,"335559685":720,"335559739":160,"335559740":240}'> </span></p>
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<h5>Stay up to date</h5>
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||
<p><span data-contrast="none">Follow us on social </span><a href="https://twitter.com/ncbi"><span data-contrast="none">@NCBI</span></a><span data-contrast="none"> and </span><a href="https://public.govdelivery.com/accounts/USNLMOCPL/subscriber/new?topic_id=USNLMOCPL_52"><span data-contrast="none">join our mailing list</span></a><span data-contrast="none"> to keep up to date with NCBI news.</span><span data-ccp-props='{"134233117":true,"134233118":true,"201341983":0,"335559739":160,"335559740":240}'> </span></p>
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||
<h5>Questions?</h5>
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||
<p><span data-contrast="none">Feel free to contact our help desk at </span><a href="mailto:blast-help@ncbi.nlm.nih.gov"><span data-contrast="none">info@ncbi.nlm.nih.gov</span></a><span data-contrast="none"> if you have any questions or concerns. </span><span data-ccp-props='{"134233117":true,"134233118":true,"201341983":0,"335559739":160,"335559740":240}'> </span></p>
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