Literature DB >> 18428716

RNA secondary structure analysis using the Vienna RNA package.

Ivo L Hofacker1.   

Abstract

This Current Protocols in Bioinformatics 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, and sequence design.

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Substances：

Year:  2004        PMID： 18428716     DOI： 10.1002/0471250953.bi1202s04

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


  33 in total

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2.  A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA.

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3.  RNA secondary structures in a polymer-zeta model how foldings should be shaped for sparsification to establish a linear speedup.

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Journal:  J Math Biol       Date:  2015-05-23       Impact factor: 2.259

4.  Overlapping local and long-range RNA-RNA interactions modulate dengue virus genome cyclization and replication.

Authors:  Luana de Borba; Sergio M Villordo; Nestor G Iglesias; Claudia V Filomatori; Leopoldo G Gebhard; Andrea V Gamarnik
Journal:  J Virol       Date:  2015-01-14       Impact factor: 5.103

5.  RNA design rules from a massive open laboratory.

Authors:  Jeehyung Lee; Wipapat Kladwang; Minjae Lee; Daniel Cantu; Martin Azizyan; Hanjoo Kim; Alex Limpaecher; Sungroh Yoon; Adrien Treuille; Rhiju Das
Journal:  Proc Natl Acad Sci U S A       Date:  2014-01-27       Impact factor: 11.205

6.  Profiling the rainbow trout hepatic miRNAome under diet-induced hyperglycemia.

Authors:  Daniel J Kostyniuk; Lucie Marandel; Mais Jubouri; Karine Dias; Robson F de Souza; Dapeng Zhang; Christopher J Martyniuk; Stéphane Panserat; Jan A Mennigen
Journal:  Physiol Genomics       Date:  2019-07-08       Impact factor: 3.107

7.  Evidence for large complex networks of plant short silencing RNAs.

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Journal:  Blood       Date:  2009-10-30       Impact factor: 22.113

9.  Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules.

Authors:  Christine Lelandais-Brière; Loreto Naya; Erika Sallet; Fanny Calenge; Florian Frugier; Caroline Hartmann; Jérome Gouzy; Martin Crespi
Journal:  Plant Cell       Date:  2009-09-18       Impact factor: 11.277

10.  Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces.

Authors:  Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl
Journal:  Nucleic Acids Res       Date:  2016-04-19       Impact factor: 16.971
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