makeblastdb

creates BLAST databases from FASTA sequences

TLDR

Create nucleotide database

$ makeblastdb -in [sequences.fasta] -dbtype nucl -out [mydb]

Create protein database

$ makeblastdb -in [proteins.fasta] -dbtype prot -out [mydb]

Add title to database

$ makeblastdb -in [sequences.fasta] -dbtype nucl -title "[My Database]" -out [mydb]

Parse sequence IDs

$ makeblastdb -in [sequences.fasta] -dbtype nucl -parse_seqids -out [mydb]

Create with taxonomy

$ makeblastdb -in [sequences.fasta] -dbtype nucl -taxid_map [taxid.map] -out [mydb]

SYNOPSIS

makeblastdb -in fasta -dbtype type [options]

makeblastdb creates BLAST databases from FASTA sequences. These databases are required for running local BLAST searches with blastn, blastp, blastx, and related programs.
The resulting database consists of multiple files with extensions like .nhr, .nin, .nsq for nucleotide or .phr, .pin, .psq for protein.

PARAMETERS

-in file

Input FASTA file.

-dbtype type

nucl (nucleotide) or prot (protein).

-out name

Database name prefix.

-title title

Database title.

-parse_seqids

Parse sequence identifiers.

-taxid_map file

Taxonomy mapping file.

-hash_index

Create hash index.

OUTPUT FILES

$ mydb.nhr  # Header
mydb.nin  # Index
mydb.nsq  # Sequences

CAVEATS

Large sequences need significant memory. Database files must stay together. Rebuilding required when source changes.

HISTORY

makeblastdb is part of BLAST+, the successor to legacy BLAST, developed at NCBI (National Center for Biotechnology Information).