[Biojava-l] DNA assembly

[Spencer Bliven]

If you just have two contiguous sequences to align, you should just use a
global sequence alignment. See
http://biojava.org/wiki/BioJava:CookBook3:PSAfor how to do this in
BioJava, or it might be easier to just use one of the
online services for this such as http://www.ebi.ac.uk/Tools/psa/.

On the other hand, if you actually want to do genome assembly (ie from many
overlapping reads), then there are much more computationally efficient
methods. BioJava isn't really intended for large-scale genome assembly, so
you'd want to use a sequence assembly
tool<http://en.wikipedia.org/wiki/Sequence_assembly>(eg Velvet).

-Spencer


On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <
khalil.elmazouari at gmail.com> wrote:

> Hi,
>
> I would like to assemble 2 overlapping DNA sequences. Is there something
> in biojava that may help in this task?
>
> Thanks
>
>
>
>
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