BlastXtract

BlastXtract – a new way of exploring translated searches

What is BlastXtract?

Searches of translated un-annotated genomic DNA sequences against protein databases is a useful early-stage method for discovering protein homologues encoded by the sequence, but generates huge amounts of output data that quickly becomes impregnable. BlastXtract is a web-based tool for managing and visualizing results from large translated BLAST and FastA searches. It combines the speed and storage benefits of Relational Database Management Systems with an easy-to-use graphical navigation map, and greatly facilitates the early exploration of genomic sequence.

How does it work?

BlastXtract uploads output data from mainly translated BLAST and FastA searches into a database, where it can be further queried and visualized through an intuitive and clickable navigation map. The best way to explore BlastXtract is to try the program yourself on an already uploaded set of Blast and FastA data. You can access a demo version here (upload function disabled, only for browsing). A MySQL dump of the underlying demo tables is also available.

How do I download and install it?

Download the latest version of BlastXtract and follow the installation instructions in the included README file.

What are the requirements?

BlastXtract is developed using Perl 5.8.0 on the Linux RedHat 9.0 operating system, but should work on most Linux or UNIX systems as long as the following required Perl modules are properly installed:

Module	Version (or higher)
Bioperl	1.4
CGI	3.05
CGI::Session	3.95
DBI	1.42
DBD::mysql / DBD::Pg	2.9003 / 1.22
SVG	2.28
GD	2.12
GD::Text	0.86
GD::Graph	1.43
GD::SVG	0.25

Also MySQL ≥ ver 3.23 or PostgreSQL ≥ ver 7.2 is needed as well as Apache web server ≥ ver 2.0.

BlastXtract is open source and protected by the GNU General Public License (GPL).

Contact details

If you have any questions, complaints, or suggestions, please email them to Marcus Claesson, Microbiology Department, University College Cork, Ireland.