[Biojava-l] About ORFs

[Mark Schreiber]

Hi -

For a 'manual' of biojava, take a look at the documentation section of
the biojava wiki (www.biojava.org). Specifically the tutorial
(http://biojava.org/wiki/BioJava:Tutorial) and the cookbook
(http://biojava.org/wiki/BioJava:CookBook).

There is more than one way to get an ORF prediction. One way would be
to do a six frame translation
(http://biojava.org/wiki/BioJava:Cookbook:Translation:SixFrames) a
more sophisticated way would be to make a Hidden Markov Model that
distinguishes coding ORFs from non coding ORFs. You could do this
using the DP package. There is no specific tutorial but you can get
some hints from the Dynamic Programming part of the cookbook.

One of the interesting things about BioJava is that it is much more
low level than something like EMBOSS. Rather than doing lots of things
it enables you to write your own programs to do things.

Hope this helps. Welcome to BioJava.

- Mark

On Sun, Mar 23, 2008 at 2:42 PM, Kuan Yang <yangkuan81 at gmail.com> wrote:
> Hi Guys,
>
> I am new to biojava and don't know how to do a lot of things with it.
> One of them is how to get ORF prediction with it. Any help will be
> appreciated.
> BTW, Is there a detailed manual for it?
>
> Thanks
>
> Kuan
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