{"id":12722,"date":"2024-01-25T13:12:00","date_gmt":"2024-01-25T18:12:00","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=12722"},"modified":"2024-01-25T13:12:00","modified_gmt":"2024-01-25T18:12:00","slug":"blast-fasta-unavailable-on-ftp","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/01\/25\/blast-fasta-unavailable-on-ftp\/","title":{"rendered":"BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024"},"content":{"rendered":"
In April 2024, the FASTA (sequence text) files of the sequences in the <\/span>Basic Alignment Search Tool (BLAST)<\/span><\/a> databases will no longer be available on the 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\u2019s taxonomy IDs for specific organisms or groups.\u00a0 <\/span>\u00a0<\/span><\/p>\n See the examples below and the <\/span>BLAST Command Line Applications User Manual<\/span><\/a> for more details on the standalone BLAST programs and working with the BLAST databases.<\/span>\u00a0<\/span><\/p>\n Note: Use <\/span>NCBI Taxonomy<\/span><\/a> to look up IDs for organisms or taxonomic groups.<\/span>\u00a0<\/span><\/p>\n Follow us on social <\/span>@NCBI<\/span><\/a>\u202fand\u202f<\/span>join our mailing list<\/span><\/a>\u202fto keep up to date with NCBI news.<\/span>\u00a0<\/span><\/p>\n Feel free to contact our help desk at\u202f<\/span>info@ncbi.nlm.nih.gov<\/span><\/a>\u202fif you have any questions or concerns.\u202f<\/span>\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":" Easily generate BLAST FASTA files yourself!\u00a0 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<\/span> Example command-lines<\/span>\u00a0<\/span><\/h5>\n
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blastdbcmd -db nt -entry all -out nt.fsa\u00a0<\/span><\/pre>\n
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blastdbcmd -db refseq_protein -taxids 9443 -target_only\u00a0 -out refseq_prot.primates.fsa\u00a0<\/span><\/pre>\n
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