blastdbcmd

Extract sequences from BLAST databases

TLDR

Get database information

$ blastdbcmd -db [nr] -info

List available databases in a path

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

Extract a sequence by accession

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

Extract all sequences from database

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

Extract sequences from a list file

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

Get sequence in specific format

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

Show BLAST database search path

$ blastdbcmd -show_blastdb_search_path

Get taxonomy information

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

SYNOPSIS

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.

PARAMETERS

-db name

BLAST database name or path

-entry id

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

-entry_batch file

File containing list of sequence identifiers

-out file

Output file (default: stdout).

-outfmt format

Custom output format string using % tokens.

-info

Display database information (type, number of sequences, total length, date).

-list path

List databases in specified path.

-recursive

Search directories recursively (with -list).

-show_blastdb_search_path

Display BLAST database search paths.

-dbtype type

Database type: nucl (nucleotide) or prot (protein). Needed when both types share a name.

-target_only

Retrieve only target sequences (no redundant group members).

-tax_info

Display taxonomy information (requires taxonomy database).

-range start-stop

Extract subsequence range (1-based, inclusive).

-strand strand

Strand to retrieve: plus or minus (nucleotide only).

-line_length N

Line length for FASTA output (default: 80). Use 0 for single-line sequences.

-long_seqids

Use long sequence identifiers including database and accession.version.

OUTPUT FORMAT TOKENS

%a - Accession%g - GI number%o - OID (ordinal ID)%t - Title (definition line)%s - Sequence data%l - Sequence length%T - Taxonomy ID%S - Scientific name%L - Common name%m - Masking data%h - Hash value%e - Membership integer

ENVIRONMENT

BLASTDB

Colon-separated list of directories to search for BLAST databases.

CAVEATS

Requires pre-formatted BLAST databases created by makeblastdb or downloaded from NCBI. Taxonomy information requires the BLAST taxonomy database (taxdb.btd/bti) to be installed. Large extractions may require significant time and disk space. The -range option uses 1-based inclusive coordinates.