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Genome Res. 2018 Jul;28(7):1079-1089. doi: 10.1101/gr.230615.117. Epub 2018 May 17.

Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.

Author information

1
Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech, Atlanta, Georgia 30332, USA.
2
Gene Probe, Incorporated, Atlanta, Georgia 30324, USA.
3
School of Computational Science and Engineering, Georgia Tech, Atlanta, Georgia 30332, USA.
4
School of Biological Sciences, Georgia Tech, Atlanta, Georgia 30332, USA.
5
Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, 141700, Russia.

Abstract

In a conventional view of the prokaryotic genome organization, promoters precede operons and ribosome binding sites (RBSs) with Shine-Dalgarno consensus precede genes. However, recent experimental research suggesting a more diverse view motivated us to develop an algorithm with improved gene-finding accuracy. We describe GeneMarkS-2, an ab initio algorithm that uses a model derived by self-training for finding species-specific (native) genes, along with an array of precomputed "heuristic" models designed to identify harder-to-detect genes (likely horizontally transferred). Importantly, we designed GeneMarkS-2 to identify several types of distinct sequence patterns (signals) involved in gene expression control, among them the patterns characteristic for leaderless transcription as well as noncanonical RBS patterns. To assess the accuracy of GeneMarkS-2, we used genes validated by COG (Clusters of Orthologous Groups) annotation, proteomics experiments, and N-terminal protein sequencing. We observed that GeneMarkS-2 performed better on average in all accuracy measures when compared with the current state-of-the-art gene prediction tools. Furthermore, the screening of ∼5000 representative prokaryotic genomes made by GeneMarkS-2 predicted frequent leaderless transcription in both archaea and bacteria. We also observed that the RBS sites in some species with leadered transcription did not necessarily exhibit the Shine-Dalgarno consensus. The modeling of different types of sequence motifs regulating gene expression prompted a division of prokaryotic genomes into five categories with distinct sequence patterns around the gene starts.

PMID:
29773659
PMCID:
PMC6028130
DOI:
10.1101/gr.230615.117
[Indexed for MEDLINE]
Free PMC Article

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