[Bioperl-l] BLAST output parsing
swapnatbhat at gmail.com
Wed Oct 31 23:49:45 EDT 2007
which -m option do you think will be helpful.
Torsten Seemann wrote:
>> I am new to bioperl. I did BLAST search of ~4000 genes and I need to
>> it. I did use -m 9 option to get a tabular information of the blast
>> But it does not include the gene names or the names of the organisms of
>> 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
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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