miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data
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
Genome Biology 2010, 11:R39 doi:10.1186/gb-2010-11-4-r39Published: 6 April 2010
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.