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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