186 lines
No EOL
13 KiB
HTML
186 lines
No EOL
13 KiB
HTML
<?xml version="1.0" encoding="UTF-8"?><rss version="2.0"
|
|
xmlns:content="http://purl.org/rss/1.0/modules/content/"
|
|
xmlns:dc="http://purl.org/dc/elements/1.1/"
|
|
xmlns:atom="http://www.w3.org/2005/Atom"
|
|
xmlns:sy="http://purl.org/rss/1.0/modules/syndication/"
|
|
|
|
>
|
|
<channel>
|
|
<title>
|
|
Comments on: BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024 </title>
|
|
<atom:link href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/feed/" rel="self" type="application/rss+xml" />
|
|
<link>https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/</link>
|
|
<description>News about NCBI resources and events</description>
|
|
<lastBuildDate>Wed, 07 Aug 2024 18:34:38 +0000</lastBuildDate>
|
|
<sy:updatePeriod>
|
|
hourly </sy:updatePeriod>
|
|
<sy:updateFrequency>
|
|
1 </sy:updateFrequency>
|
|
|
|
<item>
|
|
<title>
|
|
By: Warren Gish </title>
|
|
<link>https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-130627</link>
|
|
|
|
<dc:creator><![CDATA[Warren Gish]]></dc:creator>
|
|
<pubDate>Wed, 07 Aug 2024 18:34:38 +0000</pubDate>
|
|
<guid isPermaLink="false">https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-130627</guid>
|
|
|
|
<description><![CDATA[I believe it would be instructional for any assistance regarding this issue to be public.]]></description>
|
|
<content:encoded><![CDATA[<p>I believe it would be instructional for any assistance regarding this issue to be public.</p>
|
|
]]></content:encoded>
|
|
|
|
</item>
|
|
<item>
|
|
<title>
|
|
By: NCBI Staff </title>
|
|
<link>https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-130623</link>
|
|
|
|
<dc:creator><![CDATA[NCBI Staff]]></dc:creator>
|
|
<pubDate>Wed, 07 Aug 2024 12:36:36 +0000</pubDate>
|
|
<guid isPermaLink="false">https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-130623</guid>
|
|
|
|
<description><![CDATA[In reply to <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-130489">Bioinfo</a>.
|
|
|
|
Hello, Please contact our help desk so they can assist you: https://support.nlm.nih.gov/support/create-case/ ]]></description>
|
|
<content:encoded><![CDATA[<p>In reply to <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-130489">Bioinfo</a>.</p>
|
|
<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>
|
|
]]></content:encoded>
|
|
|
|
</item>
|
|
<item>
|
|
<title>
|
|
By: Bioinfo </title>
|
|
<link>https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-130489</link>
|
|
|
|
<dc:creator><![CDATA[Bioinfo]]></dc:creator>
|
|
<pubDate>Tue, 06 Aug 2024 08:17:17 +0000</pubDate>
|
|
<guid isPermaLink="false">https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-130489</guid>
|
|
|
|
<description><![CDATA[In reply to <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-119167">NCBI Staff</a>.
|
|
|
|
Is there any update on this?]]></description>
|
|
<content:encoded><![CDATA[<p>In reply to <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-119167">NCBI Staff</a>.</p>
|
|
<p>Is there any update on this?</p>
|
|
]]></content:encoded>
|
|
|
|
</item>
|
|
<item>
|
|
<title>
|
|
By: NCBI Staff </title>
|
|
<link>https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-119167</link>
|
|
|
|
<dc:creator><![CDATA[NCBI Staff]]></dc:creator>
|
|
<pubDate>Thu, 09 May 2024 13:01:21 +0000</pubDate>
|
|
<guid isPermaLink="false">https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-119167</guid>
|
|
|
|
<description><![CDATA[In reply to <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-119153">Bioinfo</a>.
|
|
|
|
Thank you for your feedback. We will pass it along to the BLAST Team.]]></description>
|
|
<content:encoded><![CDATA[<p>In reply to <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-119153">Bioinfo</a>.</p>
|
|
<p>Thank you for your feedback. We will pass it along to the BLAST Team.</p>
|
|
]]></content:encoded>
|
|
|
|
</item>
|
|
<item>
|
|
<title>
|
|
By: Bioinfo </title>
|
|
<link>https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-119153</link>
|
|
|
|
<dc:creator><![CDATA[Bioinfo]]></dc:creator>
|
|
<pubDate>Wed, 08 May 2024 14:23:13 +0000</pubDate>
|
|
<guid isPermaLink="false">https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-119153</guid>
|
|
|
|
<description><![CDATA[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.]]></description>
|
|
<content:encoded><![CDATA[<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>
|
|
]]></content:encoded>
|
|
|
|
</item>
|
|
<item>
|
|
<title>
|
|
By: Warren Gish </title>
|
|
<link>https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-117166</link>
|
|
|
|
<dc:creator><![CDATA[Warren Gish]]></dc:creator>
|
|
<pubDate>Fri, 23 Feb 2024 20:04:29 +0000</pubDate>
|
|
<guid isPermaLink="false">https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-117166</guid>
|
|
|
|
<description><![CDATA[In reply to <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-117134">Warren Gish</a>.
|
|
|
|
Another script named "pn2fa" has been added to convert a "packed" database (still in *.tar.gz files) to FASTA.
|
|
https://blast.advbiocomp.com/ncbihelper/]]></description>
|
|
<content:encoded><![CDATA[<p>In reply to <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-117134">Warren Gish</a>.</p>
|
|
<p>Another script named “pn2fa” has been added to convert a “packed” database (still in *.tar.gz files) to FASTA.<br />
|
|
<a href="https://blast.advbiocomp.com/ncbihelper/" rel="nofollow ugc">https://blast.advbiocomp.com/ncbihelper/</a></p>
|
|
]]></content:encoded>
|
|
|
|
</item>
|
|
<item>
|
|
<title>
|
|
By: Ian Korf </title>
|
|
<link>https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-117150</link>
|
|
|
|
<dc:creator><![CDATA[Ian Korf]]></dc:creator>
|
|
<pubDate>Tue, 20 Feb 2024 21:48:38 +0000</pubDate>
|
|
<guid isPermaLink="false">https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-117150</guid>
|
|
|
|
<description><![CDATA[Last I checked, compressed FASTA files are actually smaller than BLAST databases.]]></description>
|
|
<content:encoded><![CDATA[<p>Last I checked, compressed FASTA files are actually smaller than BLAST databases.</p>
|
|
]]></content:encoded>
|
|
|
|
</item>
|
|
<item>
|
|
<title>
|
|
By: wgishee45a6bb97c </title>
|
|
<link>https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-117135</link>
|
|
|
|
<dc:creator><![CDATA[wgishee45a6bb97c]]></dc:creator>
|
|
<pubDate>Mon, 19 Feb 2024 22:39:04 +0000</pubDate>
|
|
<guid isPermaLink="false">https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-117135</guid>
|
|
|
|
<description><![CDATA[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.
|
|
|
|
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.
|
|
https://blast.advbiocomp.com/ncbihelper/]]></description>
|
|
<content:encoded><![CDATA[<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>
|
|
<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 />
|
|
<a href="https://blast.advbiocomp.com/ncbihelper/" rel="nofollow ugc">https://blast.advbiocomp.com/ncbihelper/</a></p>
|
|
]]></content:encoded>
|
|
|
|
</item>
|
|
<item>
|
|
<title>
|
|
By: Warren Gish </title>
|
|
<link>https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-117134</link>
|
|
|
|
<dc:creator><![CDATA[Warren Gish]]></dc:creator>
|
|
<pubDate>Mon, 19 Feb 2024 22:28:02 +0000</pubDate>
|
|
<guid isPermaLink="false">https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-117134</guid>
|
|
|
|
<description><![CDATA[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.
|
|
|
|
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.]]></description>
|
|
<content:encoded><![CDATA[<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>
|
|
<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>
|
|
]]></content:encoded>
|
|
|
|
</item>
|
|
<item>
|
|
<title>
|
|
By: NCBI Staff </title>
|
|
<link>https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-116970</link>
|
|
|
|
<dc:creator><![CDATA[NCBI Staff]]></dc:creator>
|
|
<pubDate>Mon, 05 Feb 2024 21:48:08 +0000</pubDate>
|
|
<guid isPermaLink="false">https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-116970</guid>
|
|
|
|
<description><![CDATA[In reply to <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-116933">Lee Katz</a>.
|
|
|
|
Please write to the NCBI Help Desk: https://support.nlm.nih.gov/support/create-case/ They can help you with the details. ]]></description>
|
|
<content:encoded><![CDATA[<p>In reply to <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-116933">Lee Katz</a>.</p>
|
|
<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>
|
|
]]></content:encoded>
|
|
|
|
</item>
|
|
</channel>
|
|
</rss> |