Missing genes in the annotation of prokaryotic genomes

Background: Protein-coding gene detection in prokaryotic genomes is considered a much simpler problem than in intron-containing eukaryotic genomes. However there have been reports that prokaryotic gene finder programs have problems with small genes (either over-predicting or under-predicting). Therefore the question arises as to whether current genome annotations have systematically missing, small genes. Results: We have developed a high-performance computing methodology to investigate this problem. In this methodology we compare all ORFs larger than or equal to 33 aa from all fully-sequenced prokaryotic replicons. Based on that comparison, and using conservative criteria requiring a minimum taxonomic diversity between conserved ORFs in different genomes, we have discovered 1,153 candidate genes that are missing from current genome annotations. These missing genes are similar only to each other and do not have any strong similarity to gene sequences in public databases, with the impli...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Andrew S. Warren, Jeremy S. Archuleta, Wu-chun Feng, João Carlos Setubal
• Keywords: BMCBI 2010, Genome Annotation, Genomes, Small Genes