subject:"Re\: \[Biojava\-l\] Multiple sequence alignment"

Re: [Biojava-l] multiple sequence alignment

2004-07-11 Thread Patrick McConnell

Checkout Needleman-Wunsch algorithm part of the NeoBio package: http://neobio.sourceforge.net/ -Patrick McConnell Duke Bioinformatics Shared Resource Duke Comprehensive Cancer Center [EMAIL PROTECTED]

Re: [Biojava-l] Multiple sequence alignment

2003-07-26 Thread Matthew Pocock

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