SRNA Target Prediction Organizing Tool (SPOT) Integrates Computational and Experimental Data To Facilitate Functional Characterization of Bacterial Small RNAs.

ABSTRACT: Small RNAs (sRNAs) posttranscriptionally regulate mRNA targets, typically under conditions of environmental stress. Although hundreds of sRNAs have been discovered in diverse bacterial genomes, most sRNAs remain uncharacterized, even in model organisms. Identification of mRNA targets directly regulated by sRNAs is rate-limiting for sRNA functional characterization. To address this, we developed a computational pipeline that we named SPOT for sRNA target prediction organizing tool. SPOT incorporates existing computational tools to search for sRNA binding sites, allows filtering based on experimental data, and organizes the results into a standardized report. SPOT sensitivity (number of correctly predicted targets/number of total known targets) was equal to or exc

SUBMITTER: King AM 

PROVIDER: S-EPMC6354806 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature