TY - JOUR T1 - REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial genomes JF - bioRxiv DO - 10.1101/113530 SP - 113530 AU - Elvis Ndah AU - Veronique Jonckheere AU - Adam Giess AU - Eivind Valen AU - Gerben Menschaert AU - Petra Van Damme Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/05/02/113530.abstract N2 - Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION), a de novo algorithm that takes advantage of experimental protein translation evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation. REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds based on a growth curve model to screen for spurious ORFs. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel (small) ORFs including variants of previously annotated ORFs. Our predictions were supported by matching mass spectrometry (MS) proteomics data, sequence composition and conservation analysis. REPARATION is unique in that it makes use of experimental translation evidence to perform de novo ORF delineation in bacterial genomes irrespective of the sequence context of the reading frame. ER -