Interactive exploration of RNA22 microRNA target predictions

Bioinformatics. 2012 Dec 15;28(24):3322-3. doi: 10.1093/bioinformatics/bts615. Epub 2012 Oct 16.

Abstract

MicroRNA (miRNA) target prediction is an important problem. Given an miRNA sequence the task is to determine the identity of the messenger RNAs targeted by it, the locations within them where the interactions happen and the specifics of the formed heteroduplexes. Here, we describe a web-based application, RNA22-GUI, which we have designed and implemented for the interactive exploration and in-context visualization of predictions by RNA22, one of the popular miRNA target prediction algorithms. Central to our design has been the requirement to provide informative and comprehensive visualization that is integrated with interactive search capabilities and permits one to selectively isolate and focus on relevant information that is distilled on-the-fly from a large repository of pre-compiled predictions. RNA22-GUI is currently available for Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Caenorhabditis elegans / genetics
  • Drosophila melanogaster / genetics
  • Gene Expression Regulation
  • Humans
  • Mice
  • MicroRNAs / chemistry*
  • MicroRNAs / metabolism
  • RNA, Messenger / chemistry*
  • RNA, Messenger / metabolism
  • Sequence Analysis, RNA
  • Software*

Substances

  • MicroRNAs
  • RNA, Messenger