[Bioperl-l] Running into problems

Smithies, Russell Russell.Smithies at agresearch.co.nz
Mon Jan 30 15:38:43 EST 2012


I'd probably cheat a bit and optimise my blast parameters so there's less output to process.
Also, are you sure an e-value of 100 is what you're after? I'd be aiming much lower - probably 1e-6.
It also pays to mask repeats if you're blasting against a whole genome to cut down on the number of rubbish hits.

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Bradyjoel
> Sent: Tuesday, 31 January 2012 12:21 a.m.
> To: Bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Running into problems
> 
> 
> HI all,
> 
> I'm quite new to bioperl and tried to write a script that creates a database
> from a newly sequenced genome and then preforms a tblastn against a
> multiple protein fasta file and then creates a blast report were only the
> results that only preservers identity scores above 98%. However my script
> keeps returning numerous errors and problems and since I have only a little
> experience I cannot determine were I went wrong. I include the code that I
> got so far in the attachment. Hope someone can help.
> Regards Joel
> 
> http://old.nabble.com/file/p33228400/blast1.pl blast1.pl
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> View this message in context: http://old.nabble.com/Running-into-
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