A hybrid strategy for comprehensive annotation of the protein coding genes in prokaryotic genome

Abstract

Protein coding gene annotation errors in prokaryotic genomes are accumulating continually in bioinformatics databases, while the update rate of genome annotation can not keep up with the explosive increasing genome sequences in most cases. Hence it is critical to manually rectify the genome annotation errors. In this paper, a hybrid strategy by combing the gene ab initio predicting programs and the over annotated gene re-annotation programs is proposed for re-annotation of the protein coding genes in prokaryotic genomes. Based on this strategy, the protein coding genes in Geobacter sulfurreducens PCA is comprehensively re-annotated. As a consequence, 16 hypothetical genes are annotated as non-coding sequences and 104 missing genes are retrieved as protein coding genes. Subsequent function analysis and sequences analysis show that the predicting results are much reliable and robust. Further application to other genomes show that this work can provide alternative tools for later post-process of prokaryotic genome annotations.