[BiO BB] Running BLAST with a new scoring matrix

[Martin Gollery]

BLAST accepts nonstandard matrices with the use of the -M option, as
in the command

blastall -p blastp -d nr -i myseq.fa -M newmatrix


Best,
Marty

On Thu, Jul 28, 2011 at 9:10 PM, Dr. Achuthsankar S. Nair
<sankar.achuth at gmail.com> wrote:
> Hi
> I have developed a new scoring matrix to replace PAM, can anyone suggest how
> we can test this out in alignment tools inclusing BLAST ?
> Is there a tool which accepts user defined  scoring matrix ?
> Thanks in advance
> Achu
>
> --
>
> Dr Achuthsankar S Nair
> Director, State Inter-University  Centre for Bioinformatics
> University of Kerala, Trivandrum 695581, INDIA
> Tel (O) 471-2308759 (R) 471-2542220
> www.cbi.keralauniversity.edu
> www.achu.keralauniversity.edu
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>



-- 
--
Martin Gollery
Senior Bioinformatics Scientist
Tahoe Informatics
www.bioinformaticist.biz
www.hiddenmarkovmodels.com