Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction | Zendy

Jay E. Reeder | Zendy; Robert Giegerich | Zendy

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Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction

Author(s) -

Jay E. Reeder,

Robert Giegerich

Publication year - 2005

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/bti577

Subject(s) - sequence (biology) , computer science , algorithm , identification (biology) , imperfect , space (punctuation) , ideal (ethics) , multiple sequence alignment , sequence alignment , biology , peptide sequence , linguistics , philosophy , botany , genetics , epistemology , operating system , biochemistry , gene

The well-known Sankoff algorithm for simultaneous RNA sequence alignment and folding is currently considered an ideal, but computationally over-expensive method. Available tools implement this algorithm under various pragmatic restrictions. They are still expensive to use, and it is difficult to judge if the moderate quality of results is because of the underlying model or to its imperfect implementation.

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