Blast FASTA Data

p3-blast.pl [ options ] type blastdb

Blast the input against a specified blast database. The input should be a FASTA file. The blast database can also be a FASTA file, the input itself, or it can be a genome ID.


The positional parameters are the name of the blast program (blastn, blastp, blastx, or tblastn) followed by the file name of the blast database. If the blast database is not pre-built, it will be built in place. If the database is not found, it is presumed to be a genome ID. If the database name is omitted, the input will be blasted against itself.

The options in Input Options can be used to override the standard input.

The additional command-line options are as follows.


If specified, then the output is in the form of HSP data (see Hsp). This is the default, and is mutually exclusive with sim and tbl.


If specified, then the output is in the form of similarity data (see Sim). This parameter is mutually exclusive with hsp and tbl.


If specified, then the output is in the form of a six-column table: query ID, query description, subject ID, subject description, percent identity, and e-value.


If specified, then only the best match for each query sequence will be output.

BLAST Parameters

The following may be specified as BLAST parameters


Maximum E-value (default 1e-10).


Maximum number of returned results (before filtering). The default is to return all results.


Minimum required bit-score. The default is no minimum.


Minimum percent identity. The default is no minimum.


Minimum permissible match length (used to filter the results). The default is no filtering.