Pattern analysis of RNA secondary structure. Similarity and consensus of minimal-energy folding

D.A.M. Konings, P. Hogeweg

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

We describe an automated procedure to search for consensus structures or substructures in a set of homologous or related RNA molecules. The procedure is based on the calculation of optimal and sub-optimal secondary structures using thermodynamic rules for base-pairing by energy-minimization. A linear representation of the secondary structures of the related RNAs is used so that they can be compared and classified using standard alignment and clusterings programs. We illustrate the method by means of two sets of homologous small RNAs, U2 and U3, and a set of α-globin mRNAs and show that biologically interesting consensus structures are obtained.
Original languageEnglish
Pages (from-to)597-614
Number of pages18
JournalJournal of Molecular Biology
Volume207
Issue number3
DOIs
Publication statusPublished - 4 Nov 1989
Externally publishedYes

Keywords

  • genetic engineering
  • nonhuman
  • priority journal
  • RNA analysis
  • RNA structure

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