Genome Informatics
Online ISSN : 2185-842X
Print ISSN : 0919-9454
ISSN-L : 0919-9454
Grammatically Modeling and Predicting RNA Secondary Structures
Yasuo UEMURAAki HASEGAWASatoshi KOBAYASHITakashi YOKOMORI
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JOURNAL FREE ACCESS

1995 Volume 6 Pages 67-76

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Abstract

Tree Adjunct Grammar for RNA (TAG2RNA) is a new grammatical device to model RNA secondary structures including pseudoknots. An efficient parsing algorithm for this grammar is developed, and applied to some computational problems concerning RNA secondary structures. With this parser, we first try to predict secondary structures of RNA sequences which are known to form pseudoknots structures, and show prediction results which nicely match the known structures. Further, a (-1) frameshift grammar is constructed based on a biological observation that a (-1) frameshift might be caused from some structural features of RNA sequences. The proposed grammar is used to find candidate sequences for (-1) frameshift in Human spumaretrovirus gag and pol genes.

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© Japanese Society for Bioinformatics
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