[Biojava-l] Cookbook entry - feedback please

[Hannes Brandstätter-Müller]

In my case, the sequences were all pre-aligned, but yes, that could be
done first.

A question concerning consensus sequences: how do you handle gaps? N
(as I understood it) does not allow a gap. Is there a way to encode a
"might be gap here, or A or G"?

Hannes

On Thu, Dec 22, 2011 at 14:29, Andreas Prlic <andreas at sdsc.edu> wrote:
> Did you try to align the sequences first? That would also give you the
> number of identical nucleotides.
>
> Andreas
>
>
>
> On Thu, Dec 22, 2011 at 1:18 AM, Hannes Brandstätter-Müller
> <biojava at hannes.oib.com> wrote:
>> Hi!
>>
>> I recently ran into the problem of having 2 very similar DNA Sequences
>> and wanting to get (1) a difference count and (2) a consensus
>> sequence.
>>
>> I asked on stackoverflow and biostar.stackexchange.com for some input,
>> and the answers pointed me towards enums and a lookup table using
>> these. So I sat down and wrote that (that LUT took me quite some time,
>> I hope I did not make errors in there) and made a small class to
>> quickly get to the result.
>>
>> I post the code as cookbook page for future reference, possible
>> inclusion of the code into the library and of course, feedback.
>>
>> http://biojava.org/wiki/BioJava:CookBook:Core:SequenceCompare
>>
>> Hannes
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