Rfold: an exact algorithm for computing local base pairing probabilities | Zendy

Hisanori Kiryu | Zendy; Taishin Kin | Zendy; Kiyoshi Asai | Zendy

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Rfold: an exact algorithm for computing local base pairing probabilities

Author(s) -

Hisanori Kiryu,

Taishin Kin,

Kiyoshi Asai

Publication year - 2007

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btm591

Subject(s) - algorithm , base (topology) , constraint (computer aided design) , set (abstract data type) , computer science , sequence (biology) , software , pairing , base pair , mathematics , physics , dna , mathematical analysis , geometry , superconductivity , quantum mechanics , biology , genetics , programming language

Base pairing probability matrices have been frequently used for the analyses of structural RNA sequences. Recently, there has been a growing need for computing these probabilities for long DNA sequences by constraining the maximal span of base pairs to a limited value. However, none of the existing programs can exactly compute the base pairing probabilities associated with the energy model of secondary structures under such a constraint.

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