[Bioperl-l] BLAST output parsing

swapna26 swapnatbhat at gmail.com
Wed Oct 31 23:49:45 EDT 2007

which -m option do you think will be helpful.  


Torsten Seemann wrote:
> 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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> Bioperl-l at lists.open-bio.org
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