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 <[email protected]> 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 > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
