[Biojava-l] Creating an alignment object

[Nathan S. Haigh]

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
> >
> > ------------------------------------------------------------------------
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> >
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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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