blastdbcmd

Get database information

$ blastdbcmd -db [nr] -info

$ blastdbcmd -list [/path/to/databases] -recursive

$ blastdbcmd -db [nr] -entry [NP_001234] -out [sequence.fasta]

$ blastdbcmd -db [swissprot] -entry all -out [swissprot.fasta]

$ blastdbcmd -db [nr] -entry_batch [ids.txt] -out [sequences.fasta]

$ blastdbcmd -db [nr] -entry [NP_001234] -outfmt "%a %t %s"

$ blastdbcmd -show_blastdb_search_path

$ blastdbcmd -db [nr] -entry [NP_001234] -outfmt "%a %S %T"

blastdbcmd [-db database] [-entry id] [options]

blastdbcmd is a utility for extracting sequences and metadata from BLAST databases. It can retrieve individual sequences by accession, extract all sequences, display database statistics, and generate custom reports.
The tool is part of the NCBI BLAST+ suite and works with databases created by makeblastdb or downloaded from NCBI.

-db name

BLAST database name or path

Sequence identifier(s) to retrieve; use "all" for entire database

File containing list of sequence identifiers

Output file (default: stdout)

Custom output format string

Display database information

List databases in specified path

Search directories recursively (with -list)

Display BLAST database search paths

Display taxonomy information (requires taxonomy database)

Extract subsequence range

%a - Accession
%t - Title
%s - Sequence
%l - Sequence length
%T - Taxonomy ID
%S - Scientific name
%L - Common name

Requires pre-formatted BLAST databases. Taxonomy information requires the BLAST taxonomy database to be installed. Large extractions may require significant time and disk space.

makeblastdb(1), blastn(1), blastp(1), blastx(1)