Andreas Prlic just pointed out to me that... "Andreas Draeger provided the org.biojava.bio.alignment classes, where one can do e.g. swith waterman and needleman wunsch...".
Having just had a look at this it's very powerful and you should be able to implement SequenceAlignment with your own algorithm to construct a FlexibleAlignment object, if that's what you're ultimately intending to do. Basically you add sequences to/from a FlexibleAlignment, then insert gaps and deletions as necessary, all from the SequenceAlignment implementation which is passed as input a set of Sequence objects to align. cheers, Richard On Thu, 2006-05-11 at 15:26 +0100, Nathan S. Haigh wrote: > Sorry, I think I may have been unclear. > > For example I have an alignment file in FASTA format which looks like: > > >seq1 > ACGTTGCA > >seq2 > ATGTTGCG > >seq3 > AGGTTGCT > >seq4 > AGGTTGCC > > > How do I get this into an alignment object? Or, better still, can I create > an alignment object without specifying an alignment file, but somehow > creating the alignment by hand? Maybe create, a sequence object for each of > the above sequences and add them to an alignment object? > > Something like that! :o) > > Nath > > > -----Original Message----- > > From: Richard Holland [mailto:[EMAIL PROTECTED] > > Sent: 11 May 2006 14:56 > > To: [EMAIL PROTECTED] > > Cc: [email protected] > > Subject: Re: [Biojava-l] Creating an alignment object > > > > 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 > > --- > avast! Antivirus: Outbound message clean. > Virus Database (VPS): 0619-2, 11/05/2006 > Tested on: 11/05/2006 15:26:57 > avast! - copyright (c) 1988-2006 ALWIL Software. > http://www.avast.com > > > > > -- 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
