JAligner / News: Recent posts

Total number of downloads of JAligner releases has reached 5000 (~3 GB of bandwidth, thanks SF.Net)!

[All time Statistics: http://sourceforge.net/project/stats/index.php?group_id=88312&ugn=jaligner&type=&mode=alltime\]

BioWeka (http://www.bioweka.org/) is an extension library to the machine learning framework Weka for Bioinformatics knowledge discovery and analysis tasks.

BioWeka uses JAligner as component to perform classification based on local alignments.

RDPquery (http://simo.marsci.uga.edu/public_db/rdp_query.htm) is a Java application for retrieving taxonomic identifications for 16S rRNA prokaryotic gene sequences, and it uses JAligner to create alignments and to perform comparisons on sequence data.

RDPquery was created by Glen Dyszynski and Wade Sheldon in the Departments of Microbiology and Marine Sciences at the University of Georgia.

The Java Applet Rating Service (JARS) has rated JAligner as Top 25% with the following details:
- Presentation: 125
- Applet Perfect: 250
- Function: 200
- Originality: 200
- Total: 775 (out of a possible 1000).
(http://www.jars.com/classes/jresout.cgi?resource=12354)

JAligner (http://jaligner.sf.net) has been port to C# (http://jaligner.sf.net/naligner) by Joanns Vermorel (http://www.vermorel.com).

Vgrid (http://vgrid.sourceforge.net) incorporates JAligner into GridAligner (http://vgrid.sourceforge.net/gridaligner) to proof that a third party algorithm can be used in a grid environment without changing that code.

Vgrid (http://vgrid.sourceforge.net) is a grid computing system that allows to connect computers to share their computing power and form a virtual supercomputer.

Release 0.8 of JAligner has been referenced in the issue of September 13, 2004 of the weekly magazine BioInform <http://www.bioinform.com>. This is the second time where BioInform references JAligner.

BioInform is part of the The GenomeWeb Intelligence Network <http://www.genomeweb.com>.

STRAP <http://www.charite.de/bioinf/strap> (Editor for Multiple Sequence Alignments) has incorporated JAligner for pairwise local sequence alignment computations, STRAP is an interactive extendable and scriptable editor for large protein alignments which integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence.

Version 0.8 of JAligner has been released with major graphical user interface (GUI) enhancements including editing capabilities (cut, paste, delete...) for the sequences and logging all activities.

(JAligner is an open source Java implementation of Smith-Waterman algorithm for biological sequence alignment.)

JAligner has been referenced in this week (May 03, 2004) issue of the weekly magazine BioInform <http://www.bioinform.com> as a new open source Java implementation of the Smith-Waterman alignment algorithm under the "Downloads and Upgrades" section.

BioInform is part of the The GenomeWeb Intelligence Network <http://www.genomeweb.com>.