[Biojava-dev] Java implementation of Smith-Waterman algorithm

[Ahmed Moustafa]

Hi,

What are the Biojava's objects for the scoring matrices e.g. BLOSUMs and
PAMs?

Thanks,

Ahmed

On Mon, 13 Oct 2003, Schreiber, Mark wrote:

> Hi -
>
> Probably just convert to use BioJava Symbol and SymbolList objects. Probably everything else is OK.
>
> - Mark
>
>
> > -----Original Message-----
> > From: Ahmed Moustafa [mailto:ahmed at arbornet.org]
> > Sent: Sunday, 12 October 2003 7:06 p.m.
> > To: Schreiber, Mark
> > Cc: biojava-dev at biojava.org
> > Subject: RE: [Biojava-dev] Java implementation of
> > Smith-Waterman algorithm
> >
> >
> > Hi Mark,
> >
> > I believe the current API is reusable. Is it necessary to
> > convert the already existing implementation?
> >
> > Anyway, how can I convert my classes to biojava?
> >
> > Thanks!
> >
> > Ahmed
> >
> >
> > On Sun, 12 Oct 2003, Schreiber, Mark wrote:
> >
> > > Hi -
> > >
> > > We have traditionally done pairwise alignments using HMMs. However
> > > there have been numerous requests for an implementation of
> > > Smith-Waterman. If you want some help coverting your classes to
> > > biojava give us a yell on the list.
> > >
> > > - Mark
> > >
> > >
> > > 	-----Original Message-----
> > > 	From: Ahmed Moustafa [mailto:ahmed at arbornet.org]
> > > 	Sent: Sun 12/10/2003 9:19 a.m.
> > > 	To: biojava-dev at biojava.org
> > > 	Cc:
> > > 	Subject: [Biojava-dev] Java implementation of Smith-Waterman
> > > algorithm
> > >
> > >
> > >
> > > 	Hello,
> > >
> > > 	I am working on a Java package of implementations of
> > sequence alignment
> > > 	algorithms. I have released an implementation of Smith-Waterman
> > > 	algorithm with Gotoh's improvement. The time complexity
> > is O(n2) and the
> > > 	space complexity is O(m * n + n) .
> > >
> > > 	The package name is JAligner and it is hosted at sourceforge.net
> > > 	<http://jaligner.sourceforge.net>. There is a front-end
> > demo using Swing
> > > 	and Java Web Start.
> > >
> > > 	Could JAligner be incorporated into the BioJava project?
> > >
> > > 	Best Regards,
> > >
> > > 	Ahmed
> >
> >
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
>