AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions.

ABSTRACT:

Motivation

A core task of genomics is to identify the boundaries of protein coding genes, which may cover over 90% of a prokaryote's genome. Several programs are available for gene finding, yet it is currently unclear how well these programs perform and whether any offers superior accuracy. This is in part because there is no universal benchmark for gene finding and, therefore, most developers select their own benchmarking strategy.

Results

Here, we introduce AssessORF, a new approach for benchmarking prokaryotic gene predictions based on evidence from proteomics data and the evolutionary conservation of start and stop codons. We applied AssessORF to compare gene predictions offered by GenBank, GeneMarkS-2, Glimmer and Prodigal on genomes spanning the prokaryotic tree of lif

SUBMITTER: Korandla DR 

PROVIDER: S-EPMC7998711 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature