[Bioperl-l] BLAST output parsing

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Wed Oct 31 21:27:29 EDT 2007


Swapna,

> I am new to bioperl.  I did BLAST search of ~4000 genes and I need to parse
> it.  I did use -m 9 option to get a tabular information of the blast data.
> But it does not include the gene names or the names of the organisms of each
> hit.  Are there any parsers that can do this job ??

The -m 9 tabular output does not include gene descriptions and
organisms. It only includes the "gene id" that was present immediately
after the ">" sign in the FASTA file that was used to create the BLAST
database you specified with the -d option when you ran BLAST.

Hence, no parser will help you. You either have to re-do the BLAST
with a different -m value that includes the information you desire, or
write code to convert your gene IDs into what you want.

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University


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