BioJava itself cannot align sequences. It can only create objects that are representations of alignments generated by third-party software.
However, there is a third-party addon to BioJava called Strap, which can actually do the alignment work itself from within your Java program and return a BioJava alignment object that represents the results. It is available for download, along with an example of how to use it, from here: http://www.charite.de/bioinf/strap/biojavaInAnger_SequenceAligner.html cheers, Richard On Thu, 2006-05-11 at 14:27 +0100, Nathan S. Haigh wrote: > I'm new to Java and Biojava, but I've been having a play with writing and > interface and some classes for an app I'd like to write in Java. > > The part I'm playing around with at the moment deals with alignments and > groups of alignment positions. What is the easiest/best way to create an > alignment that I can then play around with and generate Locations from? A > self contained working example would be great because as I said, I'm really > new to java! > > Cheers > Nath > > ---------------------------------------------------------------------------- > ------ > Dr. Nathan S. Haigh > Bioinformatics PostDoctoral Research Associate > > Room B2 211 Tel: +44 (0)114 22 > 20112 > Department of Animal and Plant Sciences Mob: +44 (0)7742 533 > 569 > University of Sheffield Fax: +44 (0)114 22 > 20002 > Western Bank Web: > www.bioinf.shef.ac.uk > Sheffield > www.petraea.shef.ac.uk > S10 2TN > ---------------------------------------------------------------------------- > ------ > > --- > avast! Antivirus: Outbound message clean. > Virus Database (VPS): 0619-2, 11/05/2006 > Tested on: 11/05/2006 14:27:16 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
