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Literature DB >> 19496057

RNA secondary structure analysis using the Vienna RNA package.

Abstract

This unit documents how to use the Vienna RNA package for RNA secondary structure analysis. Possible tasks include structure prediction for single sequences, prediction of consensus structures, prediction of RNA-RNA interactions, and sequence design. (c) 2009 by John Wiley & Sons, Inc.

Mesh：

Substances：
RNA

Year: 2009 PMID： 19496057 DOI： 10.1002/0471250953.bi1202s26

Source DB: PubMed Journal: Curr Protoc Bioinformatics ISSN： 1934-3396

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Cited

36 in total

1. Identification of novel microRNA-like molecules generated from herpesvirus and host tRNA transcripts.

Authors: Tiffany A Reese; Jing Xia; L Steven Johnson; Xiang Zhou; Weixiong Zhang; Herbert W Virgin
Journal: J Virol Date: 2010-07-21 Impact factor: 5.103

Review 2. Predicting and modeling RNA architecture.

Authors: Eric Westhof; Benoît Masquida; Fabrice Jossinet
Journal: Cold Spring Harb Perspect Biol Date: 2011-02-01 Impact factor: 10.005

Review 3. Designing highly active siRNAs for therapeutic applications.

Authors: S Patrick Walton; Ming Wu; Joseph A Gredell; Christina Chan
Journal: FEBS J Date: 2010-12 Impact factor: 5.542

4. Computational identification and evolutionary relationships of the microRNA gene cluster miR-71/2 in protostomes.

Authors: Matheus de Souza Gomes; Mark T A Donoghue; Mohankumar Muniyappa; Roberta Verciano Pereira; Renata Guerra-Sá; Charles Spillane
Journal: J Mol Evol Date: 2013-06-06 Impact factor: 2.395

5. Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation.

Authors: Julie Bernauer; Xuhui Huang; Adelene Y L Sim; Michael Levitt
Journal: RNA Date: 2011-04-26 Impact factor: 4.942

6. Translation from unconventional 5' start sites drives tumour initiation.

Authors: Ataman Sendoel; Joshua G Dunn; Edwin H Rodriguez; Shruti Naik; Nicholas C Gomez; Brian Hurwitz; John Levorse; Brian D Dill; Daniel Schramek; Henrik Molina; Jonathan S Weissman; Elaine Fuchs
Journal: Nature Date: 2017-01-11 Impact factor: 49.962

RNA secondary structure analysis using the Vienna RNA package.

1. Identification of novel microRNA-like molecules generated from herpesvirus and host tRNA transcripts.

Review 2. Predicting and modeling RNA architecture.

Review 3. Designing highly active siRNAs for therapeutic applications.

4. Computational identification and evolutionary relationships of the microRNA gene cluster miR-71/2 in protostomes.

5. Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation.

6. Translation from unconventional 5' start sites drives tumour initiation.

7. MicroRNAs both promote and antagonize longevity in C. elegans.

8. Argonaute-bound small RNAs from promoter-proximal RNA polymerase II.

9. E-RNAi: a web application for the multi-species design of RNAi reagents--2010 update.

10. An Improved microRNA Annotation of the Canine Genome.