[Biojava-dev] find mutation motif

[Spencer Bliven]

One thing you could do is perform a local alignment of the regions around
each mutation (say, 5-10 nucleotides on either side, depending on the
length of motif you expect). If they do in fact all come from one motif
that should give you a sequence profile for it. Then you can map the SNP
locations back onto that profile to look for functionally important
positions.

-Spencer


On Fri, Feb 22, 2013 at 1:15 AM, Kristian Unger <
kristianunger at googlemail.com> wrote:

> Hi there,
>
> I am pretty new to Biojava since I normally do not work with
> sequencing analysis. I have the alignments from sequences from
> multiple clones and many of them show mutations that all seem to
> happen within a defined motif. How can I define that sort of common
> minimal region?
>
> Kristian
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