PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families |
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Authors: | Xu Xiang Wu Jinyu Xiao Jian Tan Yi Bao Qiyu Zhao Fangqing Li Xiaokun |
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Institution: | 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 |
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Abstract: | Summary: Malaria, one of the world's most common diseases, iscaused 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 comparativegenomics and phylogenetic analysis of Plasmodium gene families.Gene families were clustered using the Markov Cluster algorithmimplemented in TribeMCL program and could be searched usingkeywords, gene-family information, domain composition, GeneOntology and BLAST. Moreover, a number of useful bioinformaticstools were implemented to facilitate the analysis of these putativePlasmodium gene families, including gene retrieval, annotation,sequence alignment, phylogeny construction and visualization.In the current version, PlasmoGF contained 8980 sets of genefamilies derived from six malaria parasite genomes: Plasmodium.falciparum, P. berghei, P. knowlesi, P. chabaudi, P. vivax andP. yoelii. The availability of such a highly integrated systemwould be of great interest for the community of researchersworking 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
The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors. |
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