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

David Hendrix, Michael Levine, Weiyang Shi

Research output: Contribution to journalArticlepeer-review

75 Scopus citations

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.

Original languageEnglish (US)
Article numberr39
JournalGenome biology
Volume11
Issue number4
DOIs
StatePublished - Apr 6 2010

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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