Assessment of Gene Annotation Accuracy by Inferring Transcripts from RNA-Seq

Next generation sequencing is quickly changing long standing paradigms of genomics in terms of what is feasible to accomplish within a ldquoresearch life timerdquo and what is supposed to remain beyond limits of reliable experimental analysis. Sequencing and mapping of a prokaryote transcriptome can provide experimental validation for computationally predicted genes annotated in a prokaryotic genome. In this study we use the transcriptome sequencing to assess the accuracy of the public annotation of genes in a genome of important pathogen Bacillus anthracis. We show that the transcriptome data confirm existence of a number of genes missing in the annotation. Also, the transcriptome data indicate that pseudogenes, genes with frameshifts and in frame stop codons, do keep the transcriptional activity (while possessing a coding potential as well) and continue to present a challenge for accurate annotation.