Improving Gene Function Prediction Using Gene Neighborhoods. Kwangmin Choi Bioinformatics Program School of Informatics Indiana University, Bloomington, IN. Introduction : PLATCOM (A Platform for Computational Comparative Genomics).
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School of Informatics
Indiana University, Bloomington, IN
PLATCOM Web Interface Frontpage of Genome Plot
R.Overbeek et al. PNAS, 1999, Vol.96, pp.2896-2901
PCBBH : Pair of Close Bidirectional Best Hits
BBH : Bidirectional Best Hits
PCH : Pair of Close Homologs
COG : Clusters of Orthologous Genes
Tiling PathV.Koonin et al. Nucleic Acids Research, 2002, Vol.30, No.10, pp. 2212-2223
Phylogenetic TreeV.Daubin et al. Genome Research, Vol 12, Issue 7, 1080-1090
Genome Comparison Diagonal Plot: Phylogenetically-Distant Species (Z-score = over 500)
Case 2 : Rbs OperonZ-score = over 750, Intergenic Distance = 300
Case 3 : Functional CouplingZ-score = over 750, Intergenic Distance = 300