Re: Creating an alignment object

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@xxxxxxxxx]
> > Sent: 11 May 2006 14:56
> > To: n.haigh@xxxxxxxxxxxxxxx
> > Cc: biojava-l@xxxxxxxxxxxxxxxxxx
> > 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
> > > ------------------------------------------------------------------------
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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

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