Local RNA base pairing probabilities in large sequences | Zendy

Stephan Wolf | Zendy; Ivo L. Hofacker | Zendy; Peter F. Stadler | Zendy

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Local RNA base pairing probabilities in large sequences

Author(s) -

Stephan Wolf,

Ivo L. Hofacker,

Peter F. Stadler

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/btk014

Subject(s) - rna , base pair , sequence (biology) , base (topology) , coding (social sciences) , computer science , genome , computational biology , algorithm , genetics , theoretical computer science , biology , mathematics , dna , gene , statistics , mathematical analysis

The genome-wide search for non-coding RNAs requires efficient methods to compute and compare local secondary structures. Since the exact boundaries of such putative transcripts are typically unknown, arbitrary sequence windows have to be used in practice. Here we present a method for robustly computing the probabilities of local base pairs from long RNA sequences independent of the exact positions of the sequence window.

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