Literature DB >> 18428759

RNA secondary structure analysis using RNAstructure.

David H Mathews1.   

Abstract

RNAstructure is a user-friendly program for the prediction and analysis of RNA secondary structure under Microsoft Windows. This unit provides protocols for RNA secondary structure prediction and prediction of high-affinity oligonucleotide binding sites to a structured RNA target.

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Year:  2006        PMID： 18428759      PMCID： PMC4086783          DOI： 10.1002/0471250953.bi1206s13

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


  54 in total

1.  Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.

Authors:  Zhenjiang Xu; David H Mathews
Journal:  Bioinformatics       Date:  2010-12-30       Impact factor: 6.937

2.  Predicting helical coaxial stacking in RNA multibranch loops.

Authors:  Rahul Tyagi; David H Mathews
Journal:  RNA       Date:  2007-05-16       Impact factor: 4.942

3.  Thermodynamics of coaxially stacked helixes with GA and CC mismatches.

Authors:  J Kim; A E Walter; D H Turner
Journal:  Biochemistry       Date:  1996-10-29       Impact factor: 3.162

4.  Thermodynamic criteria for high hit rate antisense oligonucleotide design.

Authors:  O V Matveeva; D H Mathews; A D Tsodikov; S A Shabalina; R F Gesteland; J F Atkins; S M Freier
Journal:  Nucleic Acids Res       Date:  2003-09-01       Impact factor: 16.971

5.  Stochastic sampling of the RNA structural alignment space.

Authors:  Arif Ozgun Harmanci; Gaurav Sharma; David H Mathews
Journal:  Nucleic Acids Res       Date:  2009-05-08       Impact factor: 16.971

6.  Enzymatic approaches to probing of RNA secondary and tertiary structure.

Authors:  G Knapp
Journal:  Methods Enzymol       Date:  1989       Impact factor: 1.600

7.  Accelerating calculations of RNA secondary structure partition functions using GPUs.

Authors:  Harry A Stern; David H Mathews
Journal:  Algorithms Mol Biol       Date:  2013-11-01       Impact factor: 1.405

8.  Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.

Authors:  Andrew V Uzilov; Joshua M Keegan; David H Mathews
Journal:  BMC Bioinformatics       Date:  2006-03-27       Impact factor: 3.169

9.  siRNA target site secondary structure predictions using local stable substructures.

Authors:  Bret S E Heale; Harris S Soifer; Chauncey Bowers; John J Rossi
Journal:  Nucleic Acids Res       Date:  2005-02-18       Impact factor: 16.971

10.  Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design.

Authors:  Zhi John Lu; David H Mathews
Journal:  Nucleic Acids Res       Date:  2008-05-15       Impact factor: 16.971
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  32 in total

1.  Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling.

Authors:  William M Rockey; Frank J Hernandez; Sheng-You Huang; Song Cao; Craig A Howell; Gregory S Thomas; Xiu Ying Liu; Natalia Lapteva; David M Spencer; James O McNamara; Xiaoqin Zou; Shi-Jie Chen; Paloma H Giangrande
Journal:  Nucleic Acid Ther       Date:  2011-10       Impact factor: 5.486

2.  Interplay of primary sequence, position and secondary RNA structure determines alternative splicing of LMNA in a pre-mature aging syndrome.

Authors:  Asaf Shilo; Frances Anne Tosto; Jason W Rausch; Stuart F J Le Grice; Tom Misteli
Journal:  Nucleic Acids Res       Date:  2019-06-20       Impact factor: 16.971

3.  A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria.

Authors:  Joanna L McKenzie; Jennifer Robson; Michael Berney; Tony C Smith; Alaine Ruthe; Paul P Gardner; Vickery L Arcus; Gregory M Cook
Journal:  J Bacteriol       Date:  2012-02-24       Impact factor: 3.490

4.  Determination of the complete mitochondrial DNA sequence of Octopus minor.

Authors:  Rubin Cheng; Xiaodong Zheng; Xiangzhi Lin; Jianmin Yang; Qi Li
Journal:  Mol Biol Rep       Date:  2011-06-28       Impact factor: 2.316

5.  A Functional riboSNitch in the 3' Untranslated Region of FKBP5 Alters MicroRNA-320a Binding Efficiency and Mediates Vulnerability to Chronic Post-Traumatic Pain.

Authors:  Sarah D Linnstaedt; Kyle D Riker; Cathleen A Rueckeis; Katrina M Kutchko; Lela Lackey; Kathleen R McCarthy; Yi-Hsuan Tsai; Joel S Parker; Michael C Kurz; Phyllis L Hendry; Christopher Lewandowski; Elizabeth Datner; Claire Pearson; Brian O'Neil; Robert Domeier; Sangeeta Kaushik; Alain Laederach; Samuel A McLean
Journal:  J Neurosci       Date:  2018-08-27       Impact factor: 6.167

6.  Automated, customizable and efficient identification of 3D base pair modules with BayesPairing.

Authors:  Roman Sarrazin-Gendron; Vladimir Reinharz; Carlos G Oliver; Nicolas Moitessier; Jérôme Waldispühl
Journal:  Nucleic Acids Res       Date:  2019-04-23       Impact factor: 16.971

7.  An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interaction.

Authors:  Nilshad N Salim; Andrew L Feig
Journal:  PLoS One       Date:  2010-09-28       Impact factor: 3.752

8.  Transposable elements in disease-associated cryptic exons.

Authors:  Igor Vorechovsky
Journal:  Hum Genet       Date:  2009-10-10       Impact factor: 4.132

9.  A variable homopolymeric G-repeat defines small RNA-mediated posttranscriptional regulation of a chemotaxis receptor in Helicobacter pylori.

Authors:  Sandy R Pernitzsch; Stephan M Tirier; Dagmar Beier; Cynthia M Sharma
Journal:  Proc Natl Acad Sci U S A       Date:  2014-01-13       Impact factor: 11.205

10.  Hybridization thermodynamics of NimbleGen microarrays.

Authors:  Ulrike Mueckstein; Germán G Leparc; Alexandra Posekany; Ivo Hofacker; David P Kreil
Journal:  BMC Bioinformatics       Date:  2010-01-19       Impact factor: 3.169
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