Actually this leads on to the issue of how the DP package does a pairwise alignment between two protein sequences (or does it)? Does it use some sort of PAM or BLOSUM matrix?
If it does could someone write a demo of it? - Mark > -----Original Message----- > From: Matthew Pocock [mailto:[EMAIL PROTECTED]] > Sent: Friday, 10 May 2002 12:25 a.m. > To: Schreiber, Mark > Cc: [EMAIL PROTECTED] > Subject: Re: [Biojava-l] Substitution matices > > > Schreiber, Mark wrote: > > Hi - > > > > Does Biojava contain the concept of Substitution/ > similarity matrices? > > > > If not should we put in an Interface (probably in the dp package)? > > > > Probably containing the method: > > > > double substitute(Symbol a, Symbol b) throws > IllegalSymbolException; > > > > Mark Schreiber > > Bioinformatics > > AgResearch Invermay > > PO Box 50034 > > Mosgiel > > New Zealand > > > > PH: +64 3 489 9175 > > FAX: +64 3 489 3739 > > > Hi Mark, > > Yes and no. There is no explicit substitution matrix > interface as such. > However a Count or Distribution over (e.g.) proteinXprotein will have > the desired properties. It is then a matter of interpreting the > distribution to be a substitution matrix, or the count as being > observations of substitutions. > > Is there something (other than syntactic sugar) that isn't covered by > this approach? > > Matthew > > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
