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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
