Comments on: BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024 https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/ News about NCBI resources and events Wed, 07 Aug 2024 18:34:38 +0000 hourly 1 By: Warren Gish https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-130627 Wed, 07 Aug 2024 18:34:38 +0000 https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-130627 I believe it would be instructional for any assistance regarding this issue to be public.

]]> By: NCBI Staff https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-130623 Wed, 07 Aug 2024 12:36:36 +0000 https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-130623 In reply to Bioinfo.

Hello, Please contact our help desk so they can assist you: https://support.nlm.nih.gov/support/create-case/

]]> By: Bioinfo https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-130489 Tue, 06 Aug 2024 08:17:17 +0000 https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-130489 In reply to NCBI Staff.

Is there any update on this?

]]> By: NCBI Staff https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-119167 Thu, 09 May 2024 13:01:21 +0000 https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-119167 In reply to Bioinfo.

Thank you for your feedback. We will pass it along to the BLAST Team.

]]> By: Bioinfo https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-119153 Wed, 08 May 2024 14:23:13 +0000 https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-119153 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.

]]> By: Warren Gish https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-117166 Fri, 23 Feb 2024 20:04:29 +0000 https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-117166 In reply to Warren Gish.

Another script named “pn2fa” has been added to convert a “packed” database (still in *.tar.gz files) to FASTA.
https://blast.advbiocomp.com/ncbihelper/

]]> By: Ian Korf https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-117150 Tue, 20 Feb 2024 21:48:38 +0000 https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-117150 Last I checked, compressed FASTA files are actually smaller than BLAST databases.

]]> By: wgishee45a6bb97c https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-117135 Mon, 19 Feb 2024 22:39:04 +0000 https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-117135 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/

]]> By: Warren Gish https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-117134 Mon, 19 Feb 2024 22:28:02 +0000 https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-117134 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.

]]> By: NCBI Staff https://ncbiinsights.ncbi.nlm.nih.gov/2024/01/25/blast-fasta-unavailable-on-ftp/comment-page-1/#comment-116970 Mon, 05 Feb 2024 21:48:08 +0000 https://ncbiinsights.ncbi.nlm.nih.gov/?p=12722#comment-116970 In reply to Lee Katz.

Please write to the NCBI Help Desk: https://support.nlm.nih.gov/support/create-case/ They can help you with the details.

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