Hi, That depends on several things. E.g. on the substitution matrix being used, also on what you want to align.
Here a site that suggests a combination of substitution matrix and gap penalties: ( BLOSUM62 matrix with gap opening penalty of 10 and a gap extension penalty of 0.5) http://hydra.icgeb.trieste.it/benchmark_previous/index.php?experiment=13 To also advertise some related, but ancient work of myself ;-) see: at: http://peds.oxfordjournals.org/cgi/content/full/13/8/545 Andreas http://hydra.icgeb.trieste.it/benchmark_previous/index.php?experiment=13 2009/9/29 simpleyrx <[email protected]>: > > Dear experts, > > > NeedlemanWunsch's constructive funtion in biojava is as below: > public NeedlemanWunsch(short?match, > short?replace, > short?insert, > short?delete, > short?gapExtend, > SubstitutionMatrix?subMat) > I would like to know what are the default values to used NeedlemanWunsch. > Such as how select match ,replace,insert,delete,gapExtend or subMat > parameters ? > > > -- > > > Renxiang Yan > > > > > _______________________________________________ > biojava-dev mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
