Literature DB >> 26116541

In silico discovery and modeling of non-coding RNA structure in viruses.

Walter N Moss1, Joan A Steitz2.   

Abstract

This review covers several computational methods for discovering structured non-coding RNAs in viruses and modeling their putative secondary structures. Here we will use examples from two target viruses to highlight these approaches: influenza A virus-a relatively small, segmented RNA virus; and Epstein-Barr virus-a relatively large DNA virus with a complex transcriptome. Each system has unique challenges to overcome and unique characteristics to exploit. From these particular cases, generically useful approaches can be derived for the study of additional viral targets.
Copyright © 2015 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  RNA; RNA structure; Sequence analysis; Viruses; ncRNA; ncRNA prediction

Mesh：

Substances：

Year:  2015        PMID： 26116541      PMCID： PMC4684774          DOI： 10.1016/j.ymeth.2015.06.015

Source DB:  PubMed          Journal:  Methods        ISSN： 1046-2023            Impact factor:   3.608


  90 in total

1.  A computational approach to identify genes for functional RNAs in genomic sequences.

Authors:  R J Carter; I Dubchak; S R Holbrook
Journal:  Nucleic Acids Res       Date:  2001-10-01       Impact factor: 16.971

2.  Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods.

Authors:  R R Gutell; A Power; G Z Hertz; E J Putz; G D Stormo
Journal:  Nucleic Acids Res       Date:  1992-11-11       Impact factor: 16.971

3.  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

4.  The influenza virus resource at the National Center for Biotechnology Information.

Authors:  Yiming Bao; Pavel Bolotov; Dmitry Dernovoy; Boris Kiryutin; Leonid Zaslavsky; Tatiana Tatusova; Jim Ostell; David Lipman
Journal:  J Virol       Date:  2007-10-17       Impact factor: 5.103

5.  The paradox of dual roles in the RNA world: resolving the conflict between stable folding and templating ability.

Authors:  Nikola A Ivica; Benedikt Obermayer; Gregory W Campbell; Sudha Rajamani; Ulrich Gerland; Irene A Chen
Journal:  J Mol Evol       Date:  2013-09       Impact factor: 2.395

6.  The transcriptional landscape of the mammalian genome.

Authors:  P Carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; V B Bajic; S E Brenner; S Batalov; A R R Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; T L Bailey; M Bansal; L Baxter; K W Beisel; T Bersano; H Bono; A M Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; M Gariboldi; P Georgii-Hemming; T R Gingeras; T Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; K Ikeo; A Iwama; T Ishikawa; M Jakt; A Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; G Kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; L Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; L Marchionni; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Y Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; N Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; S L Salzberg; A Sandelin; C Schneider; C Schönbach; K Sekiguchi; C A M Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; E Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; M S Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; W Hide; C Bult; S M Grimmond; R D Teasdale; E T Liu; V Brusic; J Quackenbush; C Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; M Itoh; T Kato; H Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; K Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
Journal:  Science       Date:  2005-09-02       Impact factor: 47.728

7.  BlastR--fast and accurate database searches for non-coding RNAs.

Authors:  Giovanni Bussotti; Emanuele Raineri; Ionas Erb; Matthias Zytnicki; Andreas Wilm; Emmanuel Beaudoing; Philipp Bucher; Cedric Notredame
Journal:  Nucleic Acids Res       Date:  2011-05-30       Impact factor: 16.971

8.  The reality of pervasive transcription.

Authors:  Michael B Clark; Paulo P Amaral; Felix J Schlesinger; Marcel E Dinger; Ryan J Taft; John L Rinn; Chris P Ponting; Peter F Stadler; Kevin V Morris; Antonin Morillon; Joel S Rozowsky; Mark B Gerstein; Claes Wahlestedt; Yoshihide Hayashizaki; Piero Carninci; Thomas R Gingeras; John S Mattick
Journal:  PLoS Biol       Date:  2011-07-12       Impact factor: 8.029

9.  Identification and classification of conserved RNA secondary structures in the human genome.

Authors:  Jakob Skou Pedersen; Gill Bejerano; Adam Siepel; Kate Rosenbloom; Kerstin Lindblad-Toh; Eric S Lander; Jim Kent; Webb Miller; David Haussler
Journal:  PLoS Comput Biol       Date:  2006-04-21       Impact factor: 4.475

10.  RNAalifold: improved consensus structure prediction for RNA alignments.

Authors:  Stephan H Bernhart; Ivo L Hofacker; Sebastian Will; Andreas R Gruber; Peter F Stadler
Journal:  BMC Bioinformatics       Date:  2008-11-11       Impact factor: 3.169
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  4 in total

Review 1.  Computational approaches for the discovery of splicing regulatory RNA structures.

Authors:  Ryan J Andrews; Walter N Moss
Journal:  Biochim Biophys Acta Gene Regul Mech       Date:  2019-04-29       Impact factor: 4.490

2.  Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3'-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides.

Authors:  Andrew D Kauffmann; Scott D Kennedy; Walter N Moss; Elzbieta Kierzek; Ryszard Kierzek; Douglas H Turner
Journal:  RNA       Date:  2022-01-04       Impact factor: 4.942

3.  In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs.

Authors:  Lisa Marie Simon; Edoardo Morandi; Anna Luganini; Giorgio Gribaudo; Luis Martinez-Sobrido; Douglas H Turner; Salvatore Oliviero; Danny Incarnato
Journal:  Nucleic Acids Res       Date:  2019-07-26       Impact factor: 16.971

4.  Comparative Analysis of Novel Strains of Porcine Astrovirus Type 3 in the USA.

Authors:  Franco Matias Ferreyra; Karen Harmon; Laura Bradner; Eric Burrough; Rachel Derscheid; Drew R Magstadt; Alyona Michael; Marcelo Nunes de Almeida; Loni Schumacher; Chris Siepker; Panchan Sitthicharoenchai; Gregory Stevenson; Bailey Arruda
Journal:  Viruses       Date:  2021-09-17       Impact factor: 5.048
  4 in total

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