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. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
