Inverse folding of RNA pseudoknot structures |
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Authors: | James ZM Gao Linda YM Li Christian M Reidys |
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Institution: | (1) Center for Combinatorics, LPMC-TJKLC, Nankai University, Tianjin, 300071, China |
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Abstract: | Background RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick
and G-U-base pairings (secondary structure) and additional cross-serial base pairs. These interactions are called pseudoknots and
are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching
for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure
and to analyze their induced neutral networks. Since the established inverse folding algorithms, RNAinverse, RNA-SSD as well
as INFO-RNA are limited to RNA secondary structures, we present in this paper the inverse folding algorithm Inv which can
deal with 3-noncrossing, canonical pseudoknot structures. |
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