Journal of Mathematical Biology

, Volume 56, Issue 1–2, pp 15–49 | Cite as

Computational methods in noncoding RNA research

  • Ariane Machado-LimaEmail author
  • Hernando A. del Portillo
  • Alan Mitchell Durham


Non protein-coding RNAs (ncRNAs) are a research hotspot in bioinformatics. Recent discoveries have revealed new ncRNA families performing a variety of roles, from gene expression regulation to catalytic activities. It is also believed that other families are still to be unveiled. Computational methods developed for protein coding genes often fail when searching for ncRNAs. Noncoding RNAs functionality is often heavily dependent on their secondary structure, which makes gene discovery very different from protein coding RNA genes. This motivated the development of specific methods for ncRNA research. This article reviews the main approaches used to identify ncRNAs and predict secondary structure.


Review Noncoding RNAs Secondary structure prediction Structure comparison Gene finding 


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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Ariane Machado-Lima
    • 1
    Email author
  • Hernando A. del Portillo
    • 2
    • 3
  • Alan Mitchell Durham
    • 1
  1. 1.Institute of Mathematics and StatisticsUniversity of Sao PauloSao PauloBrazil
  2. 2.Institute of Biomedical SciencesUniversity of Sao PauloSao PauloBrazil
  3. 3.Barcelona Centre for International Health Research CRESIBBarcelonaSpain

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