Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Access Highly Accessed Method

miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data

David Hendrix*, Michael Levine and Weiyang Shi*

Author Affiliations

Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, 142 LSA#3200, Berkeley, CA 94720-3200, USA

For all author emails, please log on.

Genome Biology 2010, 11:R39  doi:10.1186/gb-2010-11-4-r39

Published: 6 April 2010

Abstract

MicroRNAs (miRs) have been broadly implicated in animal development and disease. We developed a novel computational strategy for the systematic, whole-genome identification of miRs from high throughput sequencing information. This method, miRTRAP, incorporates the mechanisms of miR biogenesis and includes additional criteria regarding the prevalence and quality of small RNAs arising from the antisense strand and neighboring loci. This program was applied to the simple chordate Ciona intestinalis and identified nearly 400 putative miR loci.