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 <peters...@yahoo.co.uk> 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 > <khalil.elmazou...@gmail.com> wrote: > Hi, > > what do you mean by short sequences? NT or AA? > > Best > > Khalil > > On 17 Jan 2014, at 18:00, biojava-l-requ...@lists.open-bio.org wrote: > > > Send Biojava-l mailing list submissions to > > biojava-l@lists.open-bio.org > > > > 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 > > biojava-l-requ...@lists.open-bio.org > > > > You can reach the person managing the list at > > biojava-l-ow...@lists.open-bio.org > > > > 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 <peters...@yahoo.co.uk> > > Subject: [Biojava-l] Database search with Smith and Waterman > > To: "biojava-l@lists.open-bio.org" <biojava-l@lists.open-bio.org> > > Message-ID: > > <1389965237.13315.yahoomail...@web172703.mail.ir2.yahoo.com> > > 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 - Biojava-l@lists.open-bio.org > > 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 - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l
