Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery.

ABSTRACT: Many computational methods have been used to predict novel non-coding RNAs (ncRNAs), but none, to our knowledge, have explicitly investigated the impact of integrating existing cDNA-based Expressed Sequence Tag (EST) data that flank structural RNA predictions. To determine whether flanking EST data can assist in microRNA (miRNA) prediction, we identified genomic sites encoding putative miRNAs by combining functional RNA predictions with flanking ESTs data in a model consistent with miRNAs undergoing cleavage during maturation. In both human and mouse genomes, we observed that the inclusion of flanking ESTs adjacent to and not overlapping predicted miRNAs significantly improved the performance of various methods of miRNA prediction, including direct high-throughput sequencing of small RNA l

SUBMITTER: Krzyzanowski PM 

PROVIDER: S-EPMC3115948 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature