[Biojava-l] can BioJava do alignment ?

[mark.schreiber at novartis.com]

Hi -

You can also perform an alignment using HMMs in biojava 1.3 and 1.4. See 
the example at (http://biojava.org/wiki/BioJava:CookBook:DP:PairWise). 
This is actually the most flexible way to do it.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Ramon Medrado" <rmedrado at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
10/20/2006 01:45 AM

 
        To:     biojava <Biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] can BioJava do alignment ?


Hi,

The information is true. Biojava 1.5  has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz

and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar

and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz

I wait to have helped

-- 
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil



2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it 
can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that      BioJava 1.5 can do alignment itself (e.g., 
I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
>    is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
>    itself ?

   if it does, I downloaded the CVS view of BioJava 1.5, but could not 
find

>    any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l