Balrog: A universal protein model for prokaryotic gene prediction

PLoS Comput Biol. 2021 Feb 26;17(2):e1008727. doi: 10.1371/journal.pcbi.1008727. eCollection 2021 Feb.

Abstract

Low-cost, high-throughput sequencing has led to an enormous increase in the number of sequenced microbial genomes, with well over 100,000 genomes in public archives today. Automatic genome annotation tools are integral to understanding these organisms, yet older gene finding methods must be retrained on each new genome. We have developed a universal model of prokaryotic genes by fitting a temporal convolutional network to amino-acid sequences from a large, diverse set of microbial genomes. We incorporated the new model into a gene finding system, Balrog (Bacterial Annotation by Learned Representation Of Genes), which does not require genome-specific training and which matches or outperforms other state-of-the-art gene finding tools. Balrog is freely available under the MIT license at https://github.com/salzberg-lab/Balrog.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Computational Biology
  • Computer Simulation
  • Gene Expression Profiling*
  • Genome
  • Genome, Archaeal
  • Genome, Bacterial*
  • Genome, Microbial / genetics*
  • Genomics / methods*
  • Molecular Sequence Annotation
  • Open Reading Frames
  • Programming Languages
  • Prokaryotic Cells*
  • Protein Biosynthesis
  • Software