title: PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families.
abstract: 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.
  
  
  BACKGROUND
  PlasmoGF is freely available at http://bioinformatics.zj.cn/pgf/
authors.affiliation: School of Pharmaceutical Science/Zhejiang Provincial Key Laboratory of Biotechnology Pharmaceutical Engineering, Wenzhou Medical College, Wenzhou 325035, PR China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Xu
authors.forename: Jinyu
authors.initials: J
authors.lastname: Wu
authors.forename: Jian
authors.initials: J
authors.lastname: Xiao
authors.forename: Yi
authors.initials: Y
authors.lastname: Tan
authors.forename: Qiyu
authors.initials: Q
authors.lastname: Bao
authors.forename: Fangqing
authors.initials: F
authors.lastname: Zhao
authors.forename: Xiaokun
authors.initials: X
authors.lastname: Li
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D004247:DNA / Q000235:genetics*; D023281:Genomics / Q000379:methods; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D010961:Plasmodium / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D004247:DNA