Bioinformatic Methods to Discover Cis-regulatory Elements in mRNAs

  • Stewart G. Stevens
  • Chris M. Brown
Part of the Springer Handbooks book series (SHB)


Cis-regulatory elements play a number of important roles in determining the fate of messenger RNAs (mRNAs). Due to these elements, mRNAs may be translated with remarkable efficiency, or destroyed with little translation. Untranslated regions cover over a third of a typical human mRNA and often contain a range of regulatory elements. Some elements along with their RNA or protein binding partners are well characterized, though many are not. These require different types of bioinformatic methods for identification and discovery. The most successful techniques combine a range of information and search strategies. Useful information may include conservation across species, prior biological knowledge, known false positives, or noisy high-throughput experimental data. This chapter focuses on current successful methods designed to discover elements with high sensitivity but low false-positive rates.


Covariance Model Minimum Free Energy Element Discovery Position Weight Matrix miRNA Target Site 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.





basic local alignment search tool


coding sequence


covariance model


chromatin immunoprecipitation


deoxyribonucleic acid


expressed sequence tag


finding informative regulatory element


gene expression omnibus


hidden Markov model


iron responsive element


International Union of Pure and Applied Chemistry


K homology


multiple alignment format


multiple expectation maximization for motif elicitation


multiple EM for motif elucidation in RNAs including secondary structures


minimum free energy


National Center for Biotechnology Information


protein data bank


position weight matrix


RNA-Binding Protein DataBase


RNA immunoprecipitation chip


ribonucleic acid


RNA recognition motif


stochastic context-free grammar


structure conservation index


selenocysteine insertion sequence


systematic evolution of ligands by exponential enrichment


transcription factor binding site


University of California Santa Cruz


untranslated regions


double-strand RNA


logistic regression


messenger RNA




micro support vector regression


noncoding RNA


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Copyright information

© Springer-Verlag 2014

Authors and Affiliations

  1. 1.Department of BiochemistryUniversity of OtagoDunedinNew Zealand
  2. 2.Department of BiochemistryUniversity of OtagoDunedinNew Zealand

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