So you want to be able to take 5 alignments to a single profile HMM and produce a full alignment? I would use GappedSymbolList or GappedSequence to manage inserting gaps. Then, start with one of the alignments, take another, insert gaps so that their state-paths match up, then take the next, and so on. These profiles don't have loops, right?
Matthew --- [EMAIL PROTECTED] wrote: > Hi, > > I am aligning a set of sequences to a profile HMM. I > would like to convert the > individual alignments into one (multiple sequence) > alignment object. I tried to > build a new map for my msa by retrieving the > sequence symbollist from the > statepaths and the sequence names. The problem with > this approach is that the > symbollists differ in length and the alignments > haven't been 'zipped' to take > redundant gaps into account. > > I was wondering if biojava supports conversion of a > set of alignments into a > multiple sequence alignment so that all alignments > will have the same length. > > Thanks, > > Henry Romijn > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l ________________________________________________________________________ Want to chat instantly with your online friends? Get the FREE Yahoo! Messenger http://uk.messenger.yahoo.com/ _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
