A few new applications

By drc at Tue, Oct 16 2007 1:08am |

Just a quick round up of applications I've come across over the last few weeks.

Biological Sequence Annotation Viewer — BioSAVE is a program for visualising DNA or protein sequences and annotations thereof. Annotations is used in a very broad sense here, encompassing any annotation that may be expressed in GFF format. Has a plugin architecture to allow parsing of new file formats.

A Basic Analysis Toolkit for Biological Sequences - BATS routines are available in the form of C libraries and Perl modules. Moreover, a Perl/Tk graphical user interface is provided. If BioPerl (version 1.5.2) is installed, the GUI takes advantage of its sequence parsing capabilities.

MindSeer - A portable and extensible tool for visualization of structural and functional neuroimaging data written in Java and Java 3D. Demo and more details available here.

Comments

Tue, 2007-10-16 22:15 — GrEp

BATS isn't that impressive at first glance

BATs isn't that impressive at first glance. The armchair bioinformatics guy might find some use for it, but there aren't enough state of the art algorithm implementations to make it worth a developer's time. It might be a good base for projects in an intro to comp bio class though.

Never really read through the journal it was published in, "Algorithms for Molecular Biology", http://www.almob.org/. Some of the other recent articles look very interesting...

Wed, 2007-10-17 00:15 — drc

Algorithms for Molecular Biology

Algorithms for Molecular Biology is part of the Biomedcentral listing of an increasing number of open access journals http://www.biomedcentral.com/browse/journals/

Well worth a browse through, added to which, in the UK at least, funding bodies are starting to insist that research they fund is published in Open Access journals.

Tue, 2008-03-25 02:53 — badryan

BioSAVE - update

The Biological Sequence Annotation Viewer (BioSAVE) is probably too lightweight to write a dedicated review about it. However, a manuscript describing various real-life applications of BioSAVE is now available at BMC Bioinformatics. We were pleased and surprised to get an OS X-only software published! ;-)