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

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 n

SUBMITTER: Lomsadze A 

PROVIDER: S-EPMC6028130 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature