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 journalArticle

16 Citations (Scopus)

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

Fingerprint

Untranslated RNA
Computational methods
Eukaryota
RNA
Gene expression regulation
Genes
Long Noncoding RNA
Biological Phenomena
Gene Expression Regulation
Bioinformatics
Computational Biology
Transcriptome
Conservation
Proteins
Research

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Information Systems

Cite this

Soldà, G., Makunin, I. V., Sezerman, O. U., Corradin, A., Corti, G., & Guffanti, A. (2009). An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes. Briefings in Bioinformatics, 10(5), 475-489. https://doi.org/10.1093/bib/bbp022

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes. / Soldà, Giulia; Makunin, Igor V.; Sezerman, Osman U.; Corradin, Alberto; Corti, Giorgio; Guffanti, Alessandro.

In: Briefings in Bioinformatics, Vol. 10, No. 5, 2009, p. 475-489.

Research output: Contribution to journalArticle

Soldà, G, Makunin, IV, Sezerman, OU, Corradin, A, Corti, G & Guffanti, A 2009, 'An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes', Briefings in Bioinformatics, vol. 10, no. 5, pp. 475-489. https://doi.org/10.1093/bib/bbp022
Soldà, Giulia ; Makunin, Igor V. ; Sezerman, Osman U. ; Corradin, Alberto ; Corti, Giorgio ; Guffanti, Alessandro. / An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes. In: Briefings in Bioinformatics. 2009 ; Vol. 10, No. 5. pp. 475-489.
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