Finding Non-coding RNAs Through Genome-scale Clustering

Overview

Journal J Bioinform Comput Biol

Specialty Biology

Date 2009 Apr 3

PMID 19340921

Citations 19

Authors

Huei-Hun Tseng

Zasha Weinberg

Jeremy Gore

Ronald R Breaker

Walter L Ruzzo

Affiliations

Soon will be listed here.

Abstract

Non-coding RNAs (ncRNAs) are transcripts that do not code for proteins. Recent findings have shown that RNA-mediated regulatory mechanisms influence a substantial portion of typical microbial genomes. We present an efficient method for finding potential ncRNAs in bacteria by clustering genomic sequences based on homology inferred from both primary sequence and secondary structure. We evaluate our approach using a set of predominantly Firmicutes sequences. Our results showed that, though primary sequence based-homology search was inaccurate for diverged ncRNA sequences, through our clustering method, we were able to infer motifs that recovered nearly all members of most known ncRNA families. Hence, our method shows promise for discovering new families of ncRNA.

Citing Articles

Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites.

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rRNA Mimicry in RNA Regulation of Gene Expression.

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Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions.

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A Review of Computational Methods for Finding Non-Coding RNA Genes.

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Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers.

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