[Biojava-l] SequenceLogo

[Richard Holland]

Hello.

You need to do three things. First, you need to get your sequence
alignment. This will involve constructing one yourself, or parsing it
from a file. How you do this depends entirely on what form your
alignment data is in.

Second, you must convert your sequence alignment into a distribution.
You can do this by using DistributionTools.distOverAlignment() and
passing in your alignment:

http://biojava.org/docs/api/org/biojava/bio/dist/DistributionTools.html#distOverAlignment(org.biojava.bio.symbol.Alignment)

Lastly, you need to pass your distribution into an instance of
DistributionLogo in order to render the logo:

http://biojava.org/docs/api/org/biojava/bio/gui/DistributionLogo.html

cheers,
Richard


2008/11/6 Markus Engel <engelmark at fh-bingen.de>:
> Hi!
>
> I'm completely new and unfamiliar with the BioJava-Project.
> I'm trying to draw a sequence logo, but I have no idea how it works.
> A simple example or howto would be sufficient for the moment. At least I
> hope it is.
> If somebody could tell me, what I need and how it is done, I would be very
> grateful!
>
> best regards
> Markus Engel
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-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/