Literature DB >> 34845705

Predicting the Structure of a Viroid : Structure, Structure Distribution, Consensus Structure, and Structure Drawing.

Gerhard Steger1.   

Abstract

Viroids are small non-coding RNAs that require a special sequence and structure to be replicated and transported by the host machinery. Many of these features can be predicted and later experimentally verified. Here, we will present workflows to predict viroid structures and draw the predicted structures in a pleasing and descriptive way using recently developed software.
© 2022. Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  ConStruct; Consensus structure; Partition folding; R2R; RNAalifold; RNAfold; Sequence and structure drawing; Structure of minimum free energy; VARNA

Mesh:

Substances:

Year:  2022        PMID: 34845705     DOI: 10.1007/978-1-0716-1464-8_26

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  82 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  WebLogo: a sequence logo generator.

Authors:  Gavin E Crooks; Gary Hon; John-Marc Chandonia; Steven E Brenner
Journal:  Genome Res       Date:  2004-06       Impact factor: 9.043

3.  RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble.

Authors:  Ye Ding; Chi Yu Chan; Charles E Lawrence
Journal:  RNA       Date:  2005-08       Impact factor: 4.942

4.  STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time.

Authors:  Deniz Dalli; Andreas Wilm; Indra Mainz; Gerhard Steger
Journal:  Bioinformatics       Date:  2006-04-13       Impact factor: 6.937

5.  Inferring consensus structure from nucleic acid sequences.

Authors:  D K Chiu; T Kolodziejczak
Journal:  Comput Appl Biosci       Date:  1991-07

6.  An improved algorithm for nucleic acid secondary structure display.

Authors:  R E Bruccoleri; G Heinrich
Journal:  Comput Appl Biosci       Date:  1988-03

7.  Ultraviolet light-induced crosslinking reveals a unique region of local tertiary structure in potato spindle tuber viroid and HeLa 5S RNA.

Authors:  A D Branch; B J Benenfeld; H D Robertson
Journal:  Proc Natl Acad Sci U S A       Date:  1985-10       Impact factor: 11.205

8.  VARNA: Interactive drawing and editing of the RNA secondary structure.

Authors:  Kévin Darty; Alain Denise; Yann Ponty
Journal:  Bioinformatics       Date:  2009-04-27       Impact factor: 6.937

9.  Programmatic access to bioinformatics tools from EMBL-EBI update: 2017.

Authors:  Szymon Chojnacki; Andrew Cowley; Joon Lee; Anna Foix; Rodrigo Lopez
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

10.  GenBank.

Authors:  Dennis A Benson; Mark Cavanaugh; Karen Clark; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; Eric W Sayers
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

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