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Bioinformatics Advance Access published online on March 12, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn092
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families

Xiang Xu 1,§, Jinyu Wu 2,§, Jian Xiao 1, Yi Tan 1, Qiyu Bao 2,*, Fangqing Zhao 3,* and Xiaokun Li 1,4,*

1 School of Pharmaceutical Science/Zhejiang Provincial Key Laboratory of Biotechnology Pharmaceutical Engineering, Wenzhou Medical College, Wenzhou 325035, China;
2 Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou 325000, China;
3 Department of Biochemistry and Molecular Biology, Pennsylvania State University, Pennsylvania 16802, USA;
4 National Engineering Research Center for Gene Medicine, Jinan University, Guangzhou 510632, PR China

*To whom correspondence should be addressed. X. Li: xiaokunli{at}163.net; Q. Bao: baoqy{at}genomics.org.cn; F. Zhao: fuz3{at}psu.edu


  Abstract

Summary: Malaria, one of the world's most common diseases, is caused by the intracellular protozoan parasite known as Plasmodium. Recently, with the arrival of several malaria parasite genomes, we established an integrated system named PlasmoGF for comparative genomics and phylogenetic analysis of Plasmodium gene families. Gene families were clustered using the Markov Cluster algorithm implemented in TribeMCL programMCL-based algorithm and could be searched using keywords, gene family information, domain composition, Gene Ontology and BLAST. Moreover, a number of useful bioinformatics tools were implemented to facilitate the analysis of these putative Plasmodium gene families, including gene retrieval, annotation, sequence alignment, phylogeny construction and visualization. In the current version, PlasmoGF contained 8980 sets of gene families derived from six malaria parasite genomes: P. falciparum, P. berghei, P. knowlesi, P. chabaudi, P. vivax and P. yoelii. The availability of such a highly integrated system would be of great interest for the community of researchers working on malaria parasite phylogenomics.

Availability: PlasmoGF is freely available at http://bioinformatics.zj.cn/pgf/

Associate Editor: Dr. Jonathan Wren

§ These authors contributed equally to this work.

Received on November 23, 2007; revised on March 3, 2008; accepted on March 4, 2008

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