Project in the spotlight: JaMBW - Bioinformatics.org

J.W. Bizzaro • May 27, 2004
Project in the spotlight: JaMBW
JaMBW, the ``Java based Molecular Biologist's Workbench,'' was developed by Luca I.G. Toldo at the European Molecular Biology Laboratory of Heidelberg, with the help of Rob Beynon, Eugen Buehler, Ramu Chenna, Andrey Grigoriev, James Knight, Elizabeth Odekirk, PHD Computer Consultant Ltd., and Dirk Walther. The first public release of the Workbench is hosted here at Bioinformatics.Org:

http://bioinformatics.org/JaMBW/

The software and documentation are made available to molecular biologists to give free access to the most common bioinformatic operations, according to the project pages. ``The peculiar aspect of JaMBW, however, is to take advantage of the foremost developments in computer science in order to deliver information in a way simple to use. The latter includes, therefore, point-and-click, drag-and-drop, plug-and-play.''

The slew of online tools provided by JaMBW are among the most popular at Bioinformatics.Org. They include the following:

Sequence conversion: SeqIO

Reverse/complement/inverse your sequence

Shuffle (randomize its order) your sequence

Translate from DNA to protein

Windowed percentage composition

Feature viewer

Look at all possible ORFs

Isoelectric point

Antigenic index

Oligo calculator

Dot plot comparisons

Genetical and functional site mapping

Find DNA and protein patterns, and binding/cutting sites

Three-dimensional structure viewer

PCR primer design

Phyisical mapping calculators

Buffer calculator

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