Thermodynamic matchers for the construction of the cuckoo RNA family

RNA Biology
Jan Reinkensmeier, R Giegerich

Abstract

RNA family models describe classes of functionally related, non-coding RNAs based on sequence and structure conservation. The most important method for modeling RNA families is the use of covariance models, which are stochastic models that serve in the discovery of yet unknown, homologous RNAs. However, the performance of covariance models in finding remote homologs is poor for RNA families with high sequence conservation, while for families with high structure but low sequence conservation, these models are difficult to built in the first place. A complementary approach to RNA family modeling involves the use of thermodynamic matchers. Thermodynamic matchers are RNA folding programs, based on the established thermodynamic model, but tailored to a specific structural motif. As thermodynamic matchers focus on structure and folding energy, they unfold their potential in discovering homologs, when high structure conservation is paired with low sequence conservation. In contrast to covariance models, construction of thermodynamic matchers does not require an input alignment, but requires human design decisions and experimentation, and hence, model construction is more laborious. Here we report a case study on an RNA family that was...Continue Reading

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Citations

May 29, 2015·BMC Bioinformatics·Stefan Janssen, Robert Giegerich
Nov 7, 2017·PLoS Computational Biology·Michael F Sloma, David H Mathews

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Methods Mentioned

BETA
dRNA-seq
RNA-seq

Software Mentioned

RapidShapes
RNAfold
BLAST
Rfam
GAP
Locomotif
Proteinortho
OverDangle
IPUAC

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