Thanks for your response. My problem is easier than you though.
I simpy have to calculate the ambiguity symbol for each column. My solution is: - create a list whith a set of symbol for each column - fill the set with each symbol of each sequence - calculate the ambiguity symbols for each set of this list It works pretty well but if the sequences become too long I imagine I'll use too much memory. I'll try to find another solution using the alignment object in the framework. At the moment I don't know enough the framework to find solution of this kind with it. I'll try... Anyway thanks for your help. Eric --- [EMAIL PROTECTED] wrote: > Hi Eric - > > I'm not sure if this will solve your problem but you > could make an > Alignment object from the sequences and then use the > methods of > DistributionTools to get a Distribution object for > each position in the > Alignment. These distributions will tell you the > frequency of each base at > each position in the Alignment which you could use > to make a consensus. > You can also use DistributionTools to calculate > information or entropy at > each position. > > Alternatively you could generate a markov model that > represents the > alignment and probabilistically represents the > consensus. > > Hope this helps > > Mark > > > > Mark Schreiber > Principal Scientist (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 1 Science Park Road > #04-14 The Capricorn > Singapore 117528 > > phone +65 6722 2973 > fax +65 6722 2910 > > > > > > Eric BELLARD <[EMAIL PROTECTED]> > Sent by: [EMAIL PROTECTED] > 01/13/2004 09:35 PM > Please respond to eric > > > To: [EMAIL PROTECTED] > cc: > Subject: [Biojava-l] how to calculate > consensus from a fasta file > > > Hi, > > I'd like to first thank you all for your great job > on > this project. > > I'm using biojava in a project to store some > sequencing result. > > In my application the user upload sequences from a > fasta file, and I like to build an alignment from > it. > > With your project, I can easily parse the fasta file > and get all the sequences. > > Let's consider the sequences as lines. > I'd like to calculate the column consensus using dna > degenerate alphabet. > > Does biojava implements a way to do this? > > Thanks by advance. > > Eric > > > > __________________________________ > Do you Yahoo!? > Yahoo! Hotjobs: Enter the "Signing Bonus" > Sweepstakes > http://hotjobs.sweepstakes.yahoo.com/signingbonus > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > > > __________________________________ Do you Yahoo!? Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes http://hotjobs.sweepstakes.yahoo.com/signingbonus _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
