On application of directons to functional classification of genes in prokaryotes
Computational Biology and Chemistry
Parallel Clustering Algorithm for Large Data Sets with Applications in Bioinformatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
PFP: a computational framework for phylogenetic footprinting in prokaryotic genomes
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
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We present a new computational method for the prediction of orthologous gene groups for microbial genomes based on the prediction of co-occurrences of homologous genes. The method is inspired by the observation that homologous genes are highly likely to be orthologous if their neighboring genes are also homologous. Based on co-occurrences of homologous genes, we have grouped the (predicted) operons of 77 selected sequenced microbial genomes so that operons of the same group are highly likely to be functionally similar or related. We then cluster the homologous genes in the same operon group so that genes of the same cluster are highly likely to be similar in terms of their sequences and functions, i.e., they are predicted to be orthologous genes. By comparing our predicted orthologous gene groups with the COG assignments and NCBI annotations, we conclude that our method is promising to provide more accurate and specific predictions than the existing methods.