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

Genome Biol. 2010;11(4):R39. doi: 10.1186/gb-2010-11-4-r39. Epub 2010 Apr 6.

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.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Base Sequence
  • Ciona intestinalis / genetics
  • Computational Biology / methods*
  • Genome
  • High-Throughput Screening Assays
  • MicroRNAs / analysis*
  • MicroRNAs / chemistry
  • Molecular Sequence Data
  • Phylogeny
  • Sequence Analysis, RNA / methods*

Substances

  • MicroRNAs