[BiO BB] Running BLAST with a new scoring matrix

Mikhail Fursov mike.fursov at gmail.com
Mon Aug 1 01:19:28 EDT 2011


I know that this can easily be done with Smith Waterman algorithm:
more precise but slow in comparison with BLAST.

To check your matrix with Smith Waterman you can download UGENE tool (
http://ugene.unipro.ru ), open the sequence you want to analyze and
select "Actions->Analyze->Smith-Waterman" menu. There you will see an
option to select a custom scoring matrix.


On Fri, Jul 29, 2011 at 11:10 AM, 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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