Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses.

ABSTRACT: Transcription regulatory sequences (TRSs), which occur upstream of structural and accessory genes as well as the 5' end of a coronavirus genome, play a critical role in discontinuous transcription in coronaviruses. We introduce two problems collectively aimed at identifying these regulatory sequences as well as their associated genes. First, we formulate the TRS Identification problem of identifying TRS sites in a coronavirus genome sequence with prescribed gene locations. We introduce CORSID-A, an algorithm that solves this problem to optimality in polynomial time. We demonstrate that CORSID-A outperforms existing motif-based methods in identifying TRS sites in coronaviruses. Second, we demonstrate for the first time how TRS sites can be leveraged to identify gene locations in the coronav

SUBMITTER: Zhang C 

PROVIDER: S-EPMC9214144 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature