[Biojava-l] Biojava-l Digest, Vol 134, Issue 2

[Andreas Prlic]

Hi Shakuntala,

The method for global alignment in BioJava is Needleman Wunsch.

http://www.biojava.org/docs/api/org/biojava3/alignment/NeedlemanWunsch.html

Andreas




On Fri, Apr 18, 2014 at 3:08 AM, Shakuntala Baichoo <shakunb at uom.ac.mu>wrote:

> Hi!
> Can anyone tell me which method is used by Alignments.getAllPairsScorers to
> find the pairwise distance for global alignments? Is it the method
> described by Kimura et al?
>
> Thanks.
>
> Shakuntala
>
>
>
> On Tue, Apr 15, 2014 at 8:00 PM, <biojava-l-request at lists.open-bio.org
> >wrote:
>
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> > Today's Topics:
> >
> >    1. doubt about version... (Kelvin Vieira Kredens)
> >    2. Re: doubt about version... (Andreas Prlic)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 14 Apr 2014 16:11:49 -0300
> > From: Kelvin Vieira Kredens <kredens at gmail.com>
> > Subject: [Biojava-l] doubt about version...
> > To: biojava-l at lists.open-bio.org
> > Message-ID:
> >         <CACU5nmcdA+cRqXMDoSmgzu+eBkJSxuk=
> > ZqtHzahPHerRNB-W3A at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi, I'm a brazilian doctoral student in computer sciences.... I'm in the
> > very beginning of my studies...
> >
> > I will work with DNA datasets... with some data mining questions...
> >
> > I found this API BioJava and I want to use it... But I've a doubt about
> > what version I should use.
> >
> > the version 3 is new, but have little information about... and version 1
> is
> > older but I found lots of information...
> >
> > I'm thinking about use version 1... what will be the greatest problems I
> > will need to deal about this choice?
> >
> > Is there any source of information about version 3?
> >
> > --
> > Atenciosamente,
> >
> > Kelvin Vieira Kredens
> > ?N?o seria ci?ncia se tivesse garantias, e, francamente, seria um pouco
> > chato. Mas n?o buscar?amos algo se fosse uma causa perdida? - Rick
> > Gaitskell (f?sico procurando evid?ncias de mat?ria escura)
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 14 Apr 2014 13:59:41 -0700
> > From: Andreas Prlic <andreas at sdsc.edu>
> > Subject: Re: [Biojava-l] doubt about version...
> > To: Kelvin Vieira Kredens <kredens at gmail.com>
> > Cc: Biojava <biojava-l at lists.open-bio.org>
> > Message-ID:
> >         <
> > CALthepx81HNvpiWpn3Pbs7oDsBxaqdRyv0ogXKaJ2XYQj69-0A at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Hi Kelvin,
> >
> > It depends what specific features you want.
> >
> > Take a look at the cookbook
> >
> > http://biojava.org/wiki/BioJava:CookBook
> >
> > and also the javadoc...
> >
> > http://www.biojava.org/docs/api/index.html
> >
> > Andreas
> >
> >
> > On Mon, Apr 14, 2014 at 12:11 PM, Kelvin Vieira Kredens
> > <kredens at gmail.com>wrote:
> >
> > > Hi, I'm a brazilian doctoral student in computer sciences.... I'm in
> the
> > > very beginning of my studies...
> > >
> > > I will work with DNA datasets... with some data mining questions...
> > >
> > > I found this API BioJava and I want to use it... But I've a doubt about
> > > what version I should use.
> > >
> > > the version 3 is new, but have little information about... and version
> 1
> > is
> > > older but I found lots of information...
> > >
> > > I'm thinking about use version 1... what will be the greatest problems
> I
> > > will need to deal about this choice?
> > >
> > > Is there any source of information about version 3?
> > >
> > > --
> > > Atenciosamente,
> > >
> > > Kelvin Vieira Kredens
> > > ?N?o seria ci?ncia se tivesse garantias, e, francamente, seria um pouco
> > > chato. Mas n?o buscar?amos algo se fosse uma causa perdida? - Rick
> > > Gaitskell (f?sico procurando evid?ncias de mat?ria escura)
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >
> >
> >
> >
> > ------------------------------
> >
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> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> >
> > End of Biojava-l Digest, Vol 134, Issue 2
> > *****************************************
> >
>
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