An Ariadnes thread to the identification and annotation of noncoding RNAs in eukaryotes

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Atıf İçin Kopyala

Solda G., Makunin I. V., Sezerman O. U., Corradin A., Corti G., Guffanti A.

BRIEFINGS IN BIOINFORMATICS, cilt.10, sa.5, ss.475-489, 2009 (SCI-Expanded)

• Yayın Türü: Makale / Tam Makale
• Cilt numarası: 10 Sayı: 5
• Basım Tarihi: 2009
• Doi Numarası: 10.1093/bib/bbp022
• Dergi Adı: BRIEFINGS IN BIOINFORMATICS
• Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
• Sayfa Sayıları: ss.475-489
• Anahtar Kelimeler: small and long noncoding RNA, gene prediction, genome annotation, bioinformatics analysis, regulatory RNA, bioinformatics programming, CODING REGIONS, COMPUTATIONAL IDENTIFICATION, FUNCTIONAL ANNOTATION, TRANSCRIBED SEQUENCES, MICRORNA PRECURSORS, SECONDARY STRUCTURE, REGULATORY RNAS, GENOME, DATABASE, GENE
• Acıbadem Mehmet Ali Aydınlar Üniversitesi Adresli: Hayır

Özet

Non-protein coding RNAs (ncRNAs) have emerged as a vast and heterogeneous portion of eukaryotic transcriptomes. Several ncRNA families, either short (< 200 nucleotides, nt) or long (200nt), 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.