NAME

blast2gff.pl - Convert a BLAST result file into a GFF file

SYNOPSIS

% blast2gff.pl --blast_result_file [blast result file] 
    --reference_sequence_file  [file with reference sequences (optional)] 
    --gff_output_file [gff file name (optional)]

DESCRIPTION

This script takes a blast result file and a set of reference sequences and generates a GFF file from it, with the following form:

GroupUn.1786  tblastn drosophila_HSP 880 1035  .  +  . Drosophila_Match P91685                             

It also adds entries for reference sequences, if the --reference_sequence_file flag is used:

Group1.2  sequence  sequence  1  265115  .  + .  Sequence Group1.2                           

If the --make_dumpable flag is used, it adds information to the 9th column ("Class name") to make the alignments dumpable, e.g. Target EST:actg5.3 5 300 the query start and end sites

NOTES

This code should be considered beta. Be especially skeptical of the --make_dumpable feature, as it is it untested. Please report all bugs to the gmod-gbrowse mailing list.

COMMAND-LINE OPTIONS

--blast_result_file <blast result file>                      

(Mandatory) File with BLAST output

--reference_sequence_file <file with reference sequences>    

(Optional) FASTA formatted file with reference ("database") sequences that BLAST was run against. If specified, GFF entries for the reference sequences are created.

--gff_output_file <gff file name>                            

(Optional) Name for GFF output file. If not supplied, we will write to STDOUT.

--make_dumpable                                              

(Optional) Add information to the 9th column to make the alignments dumpable, e.g. Target EST:actg5.3 5 300 (where 5 and 300 are the query start and end sites)

SEE ALSO

Bioperl also provides BLAST to GFF capability with its scripts//utilities/search2gff.PLS script.

AUTHOR

Justin Reese

jtr4v at nospam alumni.zerospam.virginia.edu

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.