Fast alignment and comparison of RNA structures | Zendy

Tim Wiegels | Zendy; Stefan Bienert | Zendy; Andrew E. Torda | Zendy

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Fast alignment and comparison of RNA structures

Author(s) -

Tim Wiegels,

Stefan Bienert,

Andrew E. Torda

Publication year - 2013

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/btt006

Subject(s) - perl , probabilistic logic , computer science , similarity (geometry) , sequence (biology) , multiple sequence alignment , measure (data warehouse) , structural alignment , source code , sequence alignment , data mining , theoretical computer science , algorithm , artificial intelligence , programming language , biology , image (mathematics) , peptide sequence , genetics , gene

To recognize remote relationships between RNA molecules, one must be able to align structures without regard to sequence similarity. We have implemented a method, which is swift [O(n(2))], sensitive and tolerant of large gaps and insertions. Molecules are broken into overlapping fragments, which are characterized by their memberships in a probabilistic classification based on local geometry and H-bonding descriptors. This leads to a probabilistic similarity measure that is used in a conventional dynamic programming method.

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