[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.  

swapna

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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://www.nabble.com/BLAST-output-parsing-tf4728082.html#a13523150
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



More information about the Bioperl-l mailing list