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

[Schreiber, Mark]

Hi -
 
This all depends on how you want to do the output. You could produce an instance of the Alignment interface (or more likely one of its subinterfaces) that gives the alignment between the two objects and use the Annotation of the alignment to store things like the score and the matrix used.
 
Another possibility would be to return some sort of result object that would basically be a data structure holding the info you might have put in the Annotation as well as the Alignment.
 
If you are searching a whole database you may need to return several Alignments.
 
- Mark
 

	-----Original Message----- 
	From: Ahmed Moustafa [mailto:ahmed at foobox.com] 
	Sent: Mon 27/10/2003 2:21 p.m. 
	To: Schreiber, Mark 
	Cc: biojava-dev at biojava.org 
	Subject: Re: [Biojava-dev] Java implementation of Smith-Waterman algorithm
	
	

	Hi Mark,
	
	Which  object does hold the output of the alignment?
	
	Thanks,
	Ahmed
	
	Schreiber, Mark wrote:
	
	>Hi -
	>
	>Because we have traditionally used HMMs there where no scoring matrices per se, just transition and emission probabilities.
	>
	>A scoring matrix would be easy to acheive. I would suggest you start with an interface called ScoringMatrix that would have as a minimum methods like:
	>
	>String getName(); which would return Blosum60 or similar depending on the implementation.
	>int getScore(Symbol s, Symbol substitute) which returns the int score for the substitution.
	>
	>You might want to also make a ScoringMatrixFactory that can generate appropriate instances of the ScoringMatrix from an XML file or files that could be included in the Distribution.
	>
	>- Mark
	>
	>
	>       -----Original Message-----
	>       From: Ahmed Moustafa [mailto:ahmed at arbornet.org]
	>       Sent: Tue 14/10/2003 6:45 p.m.
	>       To: Schreiber, Mark
	>       Cc: biojava-dev at biojava.org
	>       Subject: RE: [Biojava-dev] Java implementation of Smith-Waterman algorithm
	>      
	>      
	>
	>       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
	> 
	>
	
	


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