[Biojava-l] Biojava-l Digest, Vol 131, Issue 3

[Khalil El Mazouari]

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 <peters337 at 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.elmazouari at 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-request at lists.open-bio.org wrote:
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> >  1. Database search with Smith and Waterman (Peter S)
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> > ----------------------------------------------------------------------
> > 
> > Message: 1
> > Date: Fri, 17 Jan 2014 13:27:17 +0000 (GMT)
> > From: Peter S <peters337 at yahoo.co.uk>
> > Subject: [Biojava-l] Database search with Smith and Waterman
> > To: "biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>
> > Message-ID:
> >     <1389965237.13315.YahooMailNeo at 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
> > 
> > 
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