An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes

Giulia Soldà, Igor V. Makunin, Osman U. Sezerman, Alberto Corradin, Giorgio Corti, Alessandro Guffanti

Research output: Contribution to journalArticlepeer-review

Abstract

Non-protein coding RNAs (ncRNAs) have emerged as a vast and heterogeneous portion of eukaryotic transcriptomes. Several ncRNA families, either short (200 nt), have been described and implicated in a variety of biological processes, from translation to gene expression regulation and nuclear trafficking. Most probably, other families are still to be discovered. Computational methods for ncRNA research require different approaches from the ones normally used in the prediction of protein-coding genes. Indeed, primary sequence alone is often insufficient to infer ncRNA functionality, whereas secondary structure and local conservation of portions of the transcript could provide useful information for both the prediction and the functional annotation of ncRNAs. Here we present an overview of computational methods and bioinformatics resources currently available for studying ncRNA genes, introducing the common themes as well as the different approaches required for long and short ncRNA identification and annotation.

Original languageEnglish
Pages (from-to)475-489
Number of pages15
JournalBriefings in Bioinformatics
Volume10
Issue number5
DOIs
Publication statusPublished - 2009

Keywords

  • Bioinformatics analysis
  • Bioinformatics programming
  • Gene prediction
  • Genome annotation
  • Regulatory RNA
  • Small and long noncoding RNA

ASJC Scopus subject areas

  • Molecular Biology
  • Information Systems

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