An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.

ABSTRACT: Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome. By extending the PeptideClassifier

SUBMITTER: Omasits U 

PROVIDER: S-EPMC5741054 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature