About: Inverse Folding of RNA Pseudoknot Structures

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Inverse Folding of RNA Pseudoknot Structures
Creator	Gao, James Li, Linda Reidys, Christian
source	ArXiv
abstract	Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and /pairGU-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, {/tt RNAinverse}, {/tt RNA-SSD} as well as {/tt INFO-RNA} are limited to RNA secondary structures, we present in this paper the inverse folding algorithm {/tt Inv} which can deal with 3-noncrossing, canonical pseudoknot structures. Results: In this paper we present the inverse folding algorithm {/tt Inv}. We give a detailed analysis of {/tt Inv}, including pseudocodes. We show that {/tt Inv} allows to design in particular 3-noncrossing nonplanar RNA pseudoknot 3-noncrossing RNA structures--a class which is difficult to construct via dynamic programming routines. {/tt Inv} is freely available at /url{http://www.combinatorics.cn/cbpc/inv.html}. Conclusions: The algorithm {/tt Inv} extends inverse folding capabilities to RNA pseudoknot structures. In comparison with {/tt RNAinverse} it uses new ideas, for instance by considering sets of competing structures. As a result, {/tt Inv} is not only able to find novel sequences even for RNA secondary structures, it does so in the context of competing structures that potentially exhibit cross-serial interactions.
has issue date	2010-03-10(xsd:dateTime)
has license	arxiv
sha1sum (hex)	466dc1e5c227ca49cd0fc535dd402f5049b9161b
resource representing a document's title	Inverse Folding of RNA Pseudoknot Structures
resource representing a document's body	covid:466dc1e5c227ca49cd0fc535dd402f5049b9161b#body_text
is schema:about of	named entity 'SPECIFIC' named entity 'RIBOZYMES' named entity 'BASE' named entity 'RNA' named entity 'ARTIFICIAL' »more»

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