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The ViennaRNA Package is software, a set of standalone programs and libraries used for predicting and analysing RNA nucleic acid secondary structures. [1] The source code for the package is released as free and open-source software and compiled binaries are available for the operating systems Linux , macOS , and Windows .
The ViennaRNA Package provides RNAinverse, an algorithm for designing sequences with desired structure. Web Server [21] RNAiFold: A complete RNA inverse folding approach based on constraint programming and implemented using OR Tools which allows for the specification of a wide range of design constraints.
Sfold is a software program developed to predict probable RNA secondary structures through structure ensemble sampling and centroid predictions [1] [2] with a focus on assessment of RNA target accessibility, [3] for major applications to the rational design of siRNAs [4] in the suppression of gene expressions, and to the identification of targets for regulatory RNAs particularly microRNAs.
Secondary structure of preQ1 class 1 riboswitch from Bacillus subtilis (Bsu) obtained from ( ) using web-based RNA structure software, viennaRNA web services where P1 and P2 are the stem region, and L1, L2 and L3 are the loop region. These two stems and three loops form H-type pseudoknot in presence of preQ1.
The first step of SELEX involves the synthesis of fully or partially randomized oligonucleotide sequences of some length flanked by defined regions which allow PCR amplification of those randomized regions and, in the case of RNA SELEX, in vitro transcription of the randomized sequence.
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