Re: Biojava-l Digest, Vol 99, Issue 12
Andreas Prlic <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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.... >>> _______________________________________________ >>> Biojava-l mailing list - [email protected] >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l