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 <[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 > -- -- Martin Gollery Senior Bioinformatics Scientist Tahoe Informatics www.bioinformaticist.biz www.hiddenmarkovmodels.com _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
