T De Oliveira1, R Miller, M Tarin, S Cassol. 1. Molecular Virology and Bioinformatics, Africa Centre/University of Natal, Durban, South Africa. toliveira@mrc.ac.za
Abstract
MOTIVATION: Sequence databases encode a wealth of information needed to develop improved vaccination and treatment strategies for the control of HIV and other important pathogens. To facilitate effective utilization of these datasets, we developed a user-friendly GDE-based LINUX interface that reduces input/output file formatting. DESIGN AND RESULTS: GDE was adapted to the Linux operating system, bioinformatics tools were integrated with microbe-specific databases, and up-to-date GDE menus were developed for several clinically important viral, bacterial and parasitic genomes. Each microbial interface was designed for local access and contains Genbank, BLAST-formatted and phylogenetic databases. AVAILABILITY: GDE-Linux is available for research purposes by direct application to the corresponding author. Application-specific menus and support files can be downloaded from (http://www.bioafrica.net).
MOTIVATION: Sequence databases encode a wealth of information needed to develop improved vaccination and treatment strategies for the control of HIV and other important pathogens. To facilitate effective utilization of these datasets, we developed a user-friendly GDE-based LINUX interface that reduces input/output file formatting. DESIGN AND RESULTS: GDE was adapted to the Linux operating system, bioinformatics tools were integrated with microbe-specific databases, and up-to-date GDE menus were developed for several clinically important viral, bacterial and parasitic genomes. Each microbial interface was designed for local access and contains Genbank, BLAST-formatted and phylogenetic databases. AVAILABILITY: GDE-Linux is available for research purposes by direct application to the corresponding author. Application-specific menus and support files can be downloaded from (http://www.bioafrica.net).
Authors: M Gordon; T De Oliveira; K Bishop; H M Coovadia; L Madurai; S Engelbrecht; E Janse van Rensburg; A Mosam; A Smith; S Cassol Journal: J Virol Date: 2003-02 Impact factor: 5.103
Authors: Ebbe S Andersen; Allan Lind-Thomsen; Bjarne Knudsen; Susie E Kristensen; Jakob H Havgaard; Elfar Torarinsson; Niels Larsen; Christian Zwieb; Peter Sestoft; Jørgen Kjems; Jan Gorodkin Journal: RNA Date: 2007-09-05 Impact factor: 4.942
Authors: Tulio de Oliveira; Susan Engelbrecht; Estrelita Janse van Rensburg; Michelle Gordon; Karen Bishop; Jan zur Megede; Susan W Barnett; Sharon Cassol Journal: J Virol Date: 2003-09 Impact factor: 5.103
Authors: Pieter Libin; Gertjan Beheydt; Koen Deforche; Stijn Imbrechts; Fossie Ferreira; Kristel Van Laethem; Kristof Theys; Ana Patricia Carvalho; Joana Cavaco-Silva; Giuseppe Lapadula; Carlo Torti; Matthias Assel; Stefan Wesner; Joke Snoeck; Jean Ruelle; Annelies De Bel; Patrick Lacor; Paul De Munter; Eric Van Wijngaerden; Maurizio Zazzi; Rolf Kaiser; Ahidjo Ayouba; Martine Peeters; Tulio de Oliveira; Luiz C J Alcantara; Zehava Grossman; Peter Sloot; Dan Otelea; Simona Paraschiv; Charles Boucher; Ricardo J Camacho; Anne-Mieke Vandamme Journal: Bioinformatics Date: 2013-05-02 Impact factor: 6.937