NAME¶

formatdb - format protein or nucleotide databases for BLAST

SYNOPSIS¶

formatdb [ -] [ -B filename] [ -F filename] [ -L filename] [ -T  filename] [ -V] [ -a] [ -b] [ -e] [ -i filename] [ -l filename] [ -n str] [ -o] [ -p F] [ -s] [ -t str] [ -v N]

DESCRIPTION¶

formatdb must be used in order to format protein or nucleotide source databases before these databases can be searched by blastall, blastpgp or MegaBLAST. The source database may be in either FASTA or ASN.1 format. Although the FASTA format is most often used as input to formatdb, the use of ASN.1 is advantageous for those who are using ASN.1 as the common source for other formats such as the GenBank report. Once a source database file has been formatted by formatdb it is not needed by BLAST. Please note that if you are going to apply periodic updates to your BLAST databases using fmerge(1), you will need to keep the source database file.

OPTIONS¶

A summary of options is included below.

-

Print usage message

-B filename

Binary Gifile produced from the Gifile specified by -F. This option specifies the name of a binary GI list file. This option should be used with the -F option. A text GI list may be specified with the -F option and the -B option will produce that GI list in binary format. The binary file is smaller and BLAST does not need to convert it, so it can be read faster.

-F filename

Gifile (file containing list of gi's) for use with -B or -L

-L filename

Create an alias file named filename, limiting the sequences searched to those specified by -F.

-T filename

Set the taxonomy IDs in ASN.1 deflines according to the table in filename.

-V

Verbose: check for non-unique string ids in the database

-a

Input file is database in ASN.1 format (otherwise FASTA is expected)

-b

ASN.1 database is binary (as opposed to ASCII text)

-e

Input is a Seq-entry. A source ASN.1 database (either text ascii or binary) may contain a Bioseq-set or just one Bioseq. In the latter case -e should be provided.

-i filename

Input file(s) for formatting

-l filename

Log file name (default = formatdb.log)

-n str

Base name for BLAST files (defaults to the name of the original FASTA file)

-o

Parse SeqID and create indexes. If the source database is in FASTA format, the database identifiers in the FASTA definition line must follow the conventions of the FASTA Defline Format.

-p F

Input is a nucleotide, not a protein.

-s

Index only by accession, not by locus. This is especially useful for sequence sets like the EST's where the accession and locus names are identical. Formatdb runs faster and produces smaller temporary files if this option is used. It is strongly recommended for EST's, STS's, GSS's, and HTGS's.

-t str

Title for database file [String]

-v N

Break up large FASTA files into `volumes' of size N million letters (4000 by default). As part of the creation of a volume, formatdb writes a new type of BLAST database file, called an alias file, with the extension `nal' or `pal'.

AUTHOR¶

The National Center for Biotechnology Information.

SEE ALSO¶

blast(1), copymat(1), formatrpsdb(1), makemat(1), /usr/share/doc/blast2/formatdb.html.