Partition function and base pairing probabilities of RNA heterodimers View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2006-01

AUTHORS

Stephan H Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F Stadler, Ivo L Hofacker

ABSTRACT

BACKGROUND: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. METHODS: The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs. RESULTS: We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures. More... »

PAGES

3

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1748-7188-1-3

DOI

http://dx.doi.org/10.1186/1748-7188-1-3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1049447594

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/16722605


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1748-7188-1-3'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1748-7188-1-3'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1748-7188-1-3'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1748-7188-1-3'


 

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