title: Genome majority vote improves gene predictions.
abstract: Recent studies have noted extensive inconsistencies in gene start sites among orthologous genes in related microbial genomes. Here we provide the first documented evidence that imposing gene start consistency improves the accuracy of gene start-site prediction. We applied an algorithm using a genome majority vote (GMV) scheme to increase the consistency of gene starts among orthologs. We used a set of validated Escherichia coli genes as a standard to quantify accuracy. Results showed that the GMV algorithm can correct hundreds of gene prediction errors in sets of five or ten genomes while introducing few errors. Using a conservative calculation, we project that GMV would resolve many inconsistencies and errors in publicly available microbial gene maps. Our simple and logical solution provides a notable advance toward accurate gene maps.
authors: Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA. mewall@lanl.gov
authors: Michael E
authors: ME
authors: Wall
authors: Sindhu
authors: S
authors: Raghavan
authors: Judith D
authors: JD
authors: Cohn
authors: John
authors: J
authors: Dunbar
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004926:Escherichia coli; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D024363:Transcription Initiation Site