We do have a Smith Waterman implementation in Biojava. However the algorithm is based on dynamic programming, which by definition is "slow" but gives you the optimal alignment...
http://biojava.org/wiki/BioJava:CookBook3:PSA#Local_alignment Andreas On Fri, Jan 17, 2014 at 9:50 AM, Peter S <[email protected]> wrote: > Thanks, I will give it a try. > > Does it mean there is no fast implementation of SW in java that I can use? > > Best, > Peter > > > > On Friday, 17 January 2014, 17:45, Khalil El Mazouari < > [email protected]> wrote: > > Hi Peter, > > give it a try with Levenshtein Distance. You can use StringUtils from > apache common lang. it has a getLevenshteinDistance method. > > best, > > Khalil > > > > On 17 Jan 2014, at 18:37, Peter S <[email protected]> wrote: > > Hi Khalil, > > > > > >By short sequence I mean 12-18 nt long. I need to make alignment against > the entire transcriptome and detect matches with up to 3 mismatches. This > is the reason I need something quite fast but sensitive at the same time. > > > > > >Many thanks, > >Peter > > > > > > > >On Friday, 17 January 2014, 17:26, Khalil El Mazouari < > [email protected]> wrote: > > > >Hi, > > > >what do you mean by short sequences? NT or AA? > > > >Best > > > >Khalil > > > >On 17 Jan 2014, at 18:00, [email protected] wrote: > > > >> Send Biojava-l mailing list submissions to > >> [email protected] > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > >> or, via email, send a message with subject or body 'help' to > >> [email protected] > >> > >> You can reach the person managing the list at > >> [email protected] > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of Biojava-l digest..." > >> > >> > >> Today's Topics: > >> > >> 1. Database search with Smith and Waterman (Peter S) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Fri, 17 Jan 2014 13:27:17 +0000 (GMT) > >> From: Peter S <[email protected]> > >> Subject: [Biojava-l] Database search with Smith and Waterman > >> > To: "[email protected]" <[email protected]> > >> Message-ID: > >> <[email protected]> > >> Content-Type: text/plain; charset=iso-8859-1 > >> > >> Dear All,? > >> > >> I'm looking for an implementation of Smith and Waterman algorithm to > use in the Java desktop application I want to develop.? > >> > >> I did find some information on pairwise aligners but what I would > ideally want to have is something similar to the SSEARCH package that can > perform alignments against a very big databases, > saved locally in a fasta format. Speed is quite important and ideally I > would need an output that I can easily parse, identifying mismatch/gap > positions etc. > >> > >> Any suggestions if there is any java implementation that would fit the > description? I will be working on short sequences so sensitivity is > crucial.? > >> > >> Thanks very much for your help, > >> Peter > >> > >> > >> ------------------------------ > >> > >> _______________________________________________ > >> Biojava-l mailing list - [email protected] > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > >> > >> End of Biojava-l Digest, Vol 131, Issue 3 > >> > ***************************************** > > > > > > > > > > > >----- > > > >Confidentiality Notice: This e-mail and any files transmitted with it are > private and confidential and are solely for the use of the addressee. It > may contain material which is legally privileged. If you are not the > addressee or the person responsible for delivering to the addressee, please > notify that you have received this e-mail in error and that any use of it > is strictly prohibited. It would be helpful if you could notify the author > by replying to it. > > > > > > > > > > > > > > > > > ----- > > Confidentiality Notice: This e-mail and any files transmitted with it are > private and confidential and are solely for the use of the addressee. It > may contain material which is legally privileged. If you are not the > addressee or the person responsible for delivering to the addressee, please > notify that you have received this e-mail in error and that any use of it > is strictly prohibited. It would be helpful if you could notify the author > by replying to it. > _______________________________________________ > 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
