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Briefings in Bioinformatics Advance Access originally published online on July 4, 2007
Briefings in Bioinformatics 2007 8(5):294-303; doi:10.1093/bib/bbm026
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Informatics challenges in structured RNA

Alain Laederach

Corresponding author. Alain Laederach, Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA 94305, USA. Tel: 650 725 4484; Fax: 650 725 3863; E-mail: alain{at}helix.stanford.edu

The world of regulatory RNAs is fast expanding into mainstream molecular biology as both a subject of intense mechanistic study and as a tool for functional characterization. The RNA world is one of complex structures that carry out catalysis, sense metabolites and synthesize proteins. The dynamic and structural nature of RNAs presents a whole new set of informatics challenges to the computational community. The ability to relate structure and dynamics to function will be key to understanding this complex world. I review several important classes of structured RNAs that present our community with a series of biologically novel informatics challenges. I also review available informatics tools that have been recently developed in the field.

Keywords: RNA, folding, informatics, riboswitch, ribosome, RNAi

Submitted: March 31, 2007. Received (in revised form): June 2, 2007.


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