[Bioperl-l] BlastPlus -Match/Mismatch scores + Gap costs

[Mark A. Jensen]

Hi Janine--
The options you need are "reward" (for the match score) and "penalty" (for the 
mismatch score). Add them to -method_args.
cheers MAJ
----- Original Message ----- 
From: "Janine Arloth" <janine.arloth at googlemail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Sunday, March 21, 2010 10:02 AM
Subject: [Bioperl-l] BlastPlus -Match/Mismatch scores + Gap costs


> Hello all,
>
> while running blast(n) I want to extend to method_arg like:
> ..
> $result = $fac->$blastprogramm_input(
> -query       => $seq,
> -outfile     => "blast.txt",
> -method_args => [
> "-num_alignments" => $num_alignments_input,
> "-evalue"         => $evalue_input,
> "-word_size"     => $word_size_input,
> "-?"                    => $match_score_input,
>                "-?"                     => $gapcosts_input
> .....
> ]
> );
> ...
>
> in Bio/Tools/BlastPlus/Config.pm I found for gap costs: bln| gapopen  and bln| 
> gapextend
> so when I have the input  value = "4 4"  , then Existence:  4 = gapaopen  and 
> Extension: 4 = gapextend ??
>
> Is there a similar usage for Match/Mismatch scores like  value="1,-2"  -> 
> match=1 and mismatch=-2??
> (I can't find it)
>
> Thanks for help.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>