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

[Andreas Prlic]

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 <peters337 at yahoo.co.uk> 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 <
> khalil.elmazouari at gmail.com> 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 <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)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> 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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> >>
> >> End of Biojava-l Digest, Vol 131, Issue 3
> >>
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