[Biojava-l] Biojava-l Digest, Vol 99, Issue 12

[Andreas Prlic]

Hi Jay,

CCing the list again, somehow I dropped it off this thread.. If I
understand your example right, you want the alignment to only span the
domain that is share between the two proteins. This suggests you would
use a local alignment, not penalizing end gaps.. If you provide some
example IDs we can be more specific...

Andreas



On Fri, Apr 15, 2011 at 11:32 AM, JAX <jayunit100 at gmail.com> wrote:
> Thanks andreas :  Is there a way to globally align to sequences using smith watermans optimal local alignment; I.e. So as to get an ideal alignment of two multi domain proteins (which only share one domain), that is gapped in such a way so as to cover the whole protein length?
>
> Sent from my iPad
>
> Sent from my iPad
>
> On Apr 15, 2011, at 2:00 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> Hi Jay,
>>
>> thanks for the suggestion. There is already a needleman wunsch and
>> smith waterman implementation available as part of the alignment
>> module. Have you seen those?
>>
>> http://biojava.org/wiki/BioJava:CookBook3:PSA
>>
>> Andreas
>>
>> On Fri, Apr 15, 2011 at 10:16 AM, Jay Vyas <jayunit100 at gmail.com> wrote:
>>> I adopted a java Needlman Wunsch for proteins and it works fine ; if someone
>>> wants to integrate it or integrate or compare it w/ biojava's implementation
>>> i can provide it just email me i will send the source .
>>>
>>> otherwise i can potentially just try to commit it to a sandbox repo if one
>>> exists....
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>