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<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 →" />
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/" class="site-logo-link" rel="home" itemprop="url"></a> <h1 class="site-title"><a href="https://ncbiinsights.ncbi.nlm.nih.gov/" rel="home">NCBI Insights</a></h1>
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<article id="post-12722" class="post-12722 post type-post status-publish format-standard hentry category-whats-new tag-blast tag-fasta tag-taxonomy">
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||
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||
<header class="entry-header">
|
||
<h1 class="entry-title">BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024</h1> </header><!-- .entry-header -->
|
||
|
||
<div class="entry-content">
|
||
<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><span id="more-12722"></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 style="font-size: 17px;">Generating FASTA file of the default nucleotide database </span></li>
|
||
</ul>
|
||
<pre>blastdbcmd -db nt -entry all -out nt.fsa<span style="font-size: 1.125rem;" data-ccp-props="{"134233117":true,"134233118":true,"201341983":0,"335559685":720,"335559739":160,"335559740":240}"> </span></pre>
|
||
<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 style="font-size: 17px;" data-contrast="auto">Generating FASTA file of primate (taxonomy ID 9443) sequences from the refseq_protein database</span></li>
|
||
</ul>
|
||
<pre><span style="font-size: 15px;">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>
|
||
<h5>Stay up to date</h5>
|
||
<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>
|
||
<h5>Questions?</h5>
|
||
<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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<ul class="post-meta"><li class="author vcard"><a class="url fn n" href="https://ncbiinsights.ncbi.nlm.nih.gov/author/ncbiinsights/">NCBI Staff</a></li><li class="posted-on"><time class="entry-date published updated" datetime="2024-01-25T13:12:00-05:00">January 25, 2024</time></li></ul><!-- .post-metadata --> <div class="meta-wrapper">
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<ul class="post-tags"><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/blast/" rel="tag">Basic Local Alignment Search Tool (BLAST)</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/fasta/" rel="tag">FASTA</a></li><li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/tag/taxonomy/" rel="tag">NCBI Taxonomy</a></li></ul><!-- .post-tags --> </div><!-- .meta-wrapper -->
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<h2 class="comments-title">
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13 thoughts on “<span>BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024</span>” </h2><!-- .comments-title -->
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-116930"><time datetime="2024-01-26T07:37:30-05:00">January 26, 2024 at 7:37 am</time></a> </div><!-- .comment-metadata -->
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<p>I believe it would be more beneficial to supply the FASTA file separately, as many tools utilize FASTA files to generate an index and perform analyses. With this update, we are introducing an additional step of extracting the index from the database and using the generated FASTA file, which may not be ideal.</p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-116933"><time datetime="2024-01-26T10:14:19-05:00">January 26, 2024 at 10:14 am</time></a> </div><!-- .comment-metadata -->
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<p>Hi, I was wondering if you could provide the current process that we could follow such that we could replicate the BLAST FTP as it is now? Could you provide the exact commands and all the minutiae like the steps for `wget` and even `mkdir`, and then of course `blastdbcmd`? If so, we could be more confident that we can create our own local database as it should be. Thank you!</p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-116947"><time datetime="2024-01-29T12:34:53-05:00">January 29, 2024 at 12:34 pm</time></a> </div><!-- .comment-metadata -->
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<p>Hello. Please write to our help desk so we can assist you with your questions: <a href="https://support.nlm.nih.gov/support/create-case/" rel="nofollow ugc">https://support.nlm.nih.gov/support/create-case/</a> </p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-116970"><time datetime="2024-02-05T16:48:08-05:00">February 5, 2024 at 4:48 pm</time></a> </div><!-- .comment-metadata -->
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<p>Please write to the NCBI Help Desk: <a href="https://support.nlm.nih.gov/support/create-case/" rel="nofollow ugc">https://support.nlm.nih.gov/support/create-case/</a> They can help you with the details. </p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-117134"><time datetime="2024-02-19T17:28:02-05:00">February 19, 2024 at 5:28 pm</time></a> </div><!-- .comment-metadata -->
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<p>I believe the NCBI has lost sight of an important part of its mission here, even if the number of users affected may be relatively small. The extra steps, computation, and storage required to produce transparent FASTA-format data will pose an unnecessary impediment to working with public datasets; and the use of NCBI tools should not be a requirement for working with these data in ways not imagined by the NCBI. Hopefully the organization changes its mind.</p>
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<p>To improve the speed of conversion of NCBI BLAST data to FASTA, a bash script named “n2fa” has been posted at the URL provided with this comment. This script utilizes parallel processing in the conversion to FASTA as well as compression of the FASTA into gzip or zstd format. The third party utilities required for the speed-up are documented in the script.</p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-117166"><time datetime="2024-02-23T15:04:29-05:00">February 23, 2024 at 3:04 pm</time></a> </div><!-- .comment-metadata -->
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<p>Another script named “pn2fa” has been added to convert a “packed” database (still in *.tar.gz files) to FASTA.<br />
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<a href="https://blast.advbiocomp.com/ncbihelper/" rel="nofollow ugc">https://blast.advbiocomp.com/ncbihelper/</a></p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-117135"><time datetime="2024-02-19T17:39:04-05:00">February 19, 2024 at 5:39 pm</time></a> </div><!-- .comment-metadata -->
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<p>I believe the NCBI has lost sight of an important part of its mission here, even if the number of users affected may be relatively small. The extra steps, computation, and storage required to produce transparent FASTA-format data will pose an unnecessary impediment to working with public datasets; and the use of NCBI tools should not be a requirement for working with these data in ways not imagined by the NCBI. Hopefully the organization changes its mind.</p>
|
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<p>To improve the speed of conversion of NCBI BLAST data to FASTA, a bash script named “n2fa” has been posted at the URL provided with this comment. This script utilizes parallel processing in the conversion to FASTA as well as compression of the FASTA into gzip or zstd format. The third party utilities required for the speed-up are documented in the script.<br />
|
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<a href="https://blast.advbiocomp.com/ncbihelper/" rel="nofollow ugc">https://blast.advbiocomp.com/ncbihelper/</a></p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-117150"><time datetime="2024-02-20T16:48:38-05:00">February 20, 2024 at 4:48 pm</time></a> </div><!-- .comment-metadata -->
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<p>Last I checked, compressed FASTA files are actually smaller than BLAST databases.</p>
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<img alt='' src='https://secure.gravatar.com/avatar/f6acda3ff19dc398b10376955ee5b50b?s=50&d=identicon&r=g' srcset='https://secure.gravatar.com/avatar/f6acda3ff19dc398b10376955ee5b50b?s=100&d=identicon&r=g 2x' class='avatar avatar-50 photo' height='50' width='50' loading='lazy' decoding='async'/> <b class="fn">Bioinfo</b> <span class="says">says:</span> </div><!-- .comment-author -->
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-119153"><time datetime="2024-05-08T10:23:13-04:00">May 8, 2024 at 10:23 am</time></a> </div><!-- .comment-metadata -->
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<p>Providing a compressed FASTA file would be more helpful, as the dependency on blastcmd is not necessary. Compressed files are smaller in size and can be downloaded faster. Currently, downloading and indexing are becoming increasingly time-consuming tasks. Additionally, several tools are not compatible with the blast index file, and blast runs (such as NCBI-blastp, blastx, etc.) are considerably slower for metagenomics datasets.</p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-119167"><time datetime="2024-05-09T09:01:21-04:00">May 9, 2024 at 9:01 am</time></a> </div><!-- .comment-metadata -->
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<p>Thank you for your feedback. We will pass it along to the BLAST Team.</p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-130489"><time datetime="2024-08-06T04:17:17-04:00">August 6, 2024 at 4:17 am</time></a> </div><!-- .comment-metadata -->
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<p>Is there any update on this?</p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-130623"><time datetime="2024-08-07T08:36:36-04:00">August 7, 2024 at 8:36 am</time></a> </div><!-- .comment-metadata -->
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<p>Hello, Please contact our help desk so they can assist you: <a href="https://support.nlm.nih.gov/support/create-case/" rel="nofollow ugc">https://support.nlm.nih.gov/support/create-case/</a> </p>
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<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/#comment-130627"><time datetime="2024-08-07T14:34:38-04:00">August 7, 2024 at 2:34 pm</time></a> </div><!-- .comment-metadata -->
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<p>I believe it would be instructional for any assistance regarding this issue to be public.</p>
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