Non-coding Transcription Characterization and Annotation: A Guide and Web Resource for Non-Coding RNA Databases

RNA Biol. 2012 Mar;9(3):274-82. doi: 10.4161/rna.19352. Epub 2012 Mar 1.

Abstract

Large-scale transcriptome projects have shown that the number of RNA transcripts not coding for proteins (non-coding RNAs) is much larger than previously recognized. High-throughput technologies, coupled with bioinformatics approaches, have produced increasing amounts of data, highlighting the role of non-coding RNAs (ncRNAs) in biological processes. Data generated by these studies include diverse non-coding RNA classes from organisms of different kingdoms, which were obtained using different experimental and computational assays. This has led to a rapid increase of specialized RNA databases. The fast growth in the number of available databases makes integration of stored information a difficult task. We present here NRDR, a Non-coding RNA Databases Resource for information retrieval on ncRNA databases (www.ncrnadatabases.org). We performed a survey of 102 public databases on ncRNAs and we have introduced four categorizations to classify these databases and to help researchers quickly search and find the information they need: RNA family, information source, information content and available search mechanisms. NRDR is a useful databases searching tool that will facilitate research on ncRNAs.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Computational Biology / methods
  • Databases, Nucleic Acid
  • Internet
  • Molecular Sequence Annotation*
  • RNA, Untranslated / classification
  • RNA, Untranslated / genetics*
  • Transcription, Genetic*

Substances

  • RNA, Untranslated