Analysis of Protean Genomics to Increase Genome Annotation Accuracy

Advances in sequencing strategies facilitate complete genomic sequence of a variety of organisms. However, conventional computational predictions for genome annotation remain imperfect. Here, we applied a protean genomics approach to complement genome annotation by combining bioinformatics analysis and proteomic data. By using Shebelle Flexner 2a as a model, a total of 1041 proteins were unambiguously assigned, including 240 hypothetical proteins. Through comprehensive analysis against in-house N-terminal extension database, three annotated open reading frames (Offs) were respectively extended upstream. Above all, eight new ORFs were discovered by searching our MS/MS data against all six possible reading frames of S. Flexner 2a str. 301 genome, which were not predicted by any other annotation approaches. Our findings indicate that protean genomic analysis is quite qualified for comprehensive and accurate genome-wide annotation. This strategy could be taken as a routine work.