[Biojava-l] Creating an alignment object

[Richard Holland]

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:richard.holland at ebi.ac.uk]
> > Sent: 11 May 2006 14:56
> > To: n.haigh at sheffield.ac.uk
> > Cc: biojava-l at lists.open-bio.org
> > 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
> > >
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> > 22
> > > 20002
> > > Western Bank                                           Web:
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> > > Sheffield
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> > --
> > Richard Holland (BioMart Team)
> > EMBL-EBI
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge CB10 1SD
> > UNITED KINGDOM
> > Tel: +44-(0)1223-494416
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-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416