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Bioinformatics Advance Access originally published online on March 12, 2008
Bioinformatics 2008 24(9):1217-1220; 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,{dagger}, Jinyu Wu 2,{dagger}, Jian Xiao 1, Yi Tan 1, Qiyu Bao 2,*, Fangqing Zhao 3,* and Xiaokun Li 1,4,*

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

*To whom correspondence should be addressed.


  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 program 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: Plasmodium. 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/

Contact: xiaokunli{at}163.net; baoqy{at}genomics.org.cn; fuz3{at}psu.edu

Associate Editor: Jonathan Wren

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

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

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