BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024

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 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.   

See the examples below and the BLAST Command Line Applications User Manual for more details on the standalone BLAST programs and working with the BLAST databases. 

Example command-lines 
  • Generating FASTA file of the default nucleotide database 
blastdbcmd -db nt -entry all -out nt.fsa 
  • Generating FASTA file of primate (taxonomy ID 9443) sequences from the refseq_protein database
blastdbcmd -db refseq_protein -taxids 9443 -target_only  -out refseq_prot.primates.fsa 

Note: Use NCBI Taxonomy to look up IDs for organisms or taxonomic groups. 

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8 thoughts on “BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024”

  1. 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.

    Reply

  2. 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!

    Reply

  3. 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.

    Reply

  4. 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/

    Reply

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