Literature DB >> 29484584

Workflow for a Computational Analysis of an sRNA Candidate in Bacteria.

Patrick R Wright1, Jens Georg2.   

Abstract

Computational methods can often facilitate the functional characterization of individual sRNAs and furthermore allow high-throughput analysis on large numbers of sRNA candidates. This chapter outlines a potential workflow for computational sRNA analyses and describes in detail methods for homolog detection, target prediction, and functional characterization based on enrichment analysis. The cyanobacterial sRNA IsaR1 is used as a specific example. All methods are available as webservers and easily accessible for nonexpert users.

Keywords:  Computational methods; Cyanobacteria; Functional characterization; IsaR1; Target prediction; sRNA conservation

Mesh：

Substances：

Year:  2018        PMID： 29484584     DOI： 10.1007/978-1-4939-7634-8_1

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


  7 in total

Review 1.  Thirty Years of sRNA-Mediated Regulation in Staphylococcus aureus: From Initial Discoveries to In Vivo Biological Implications.

Authors:  Guillaume Menard; Chloé Silard; Marie Suriray; Astrid Rouillon; Yoann Augagneur
Journal:  Int J Mol Sci       Date:  2022-07-01       Impact factor: 6.208

2.  Freiburg RNA tools: a central online resource for RNA-focused research and teaching.

Authors:  Martin Raden; Syed M Ali; Omer S Alkhnbashi; Anke Busch; Fabrizio Costa; Jason A Davis; Florian Eggenhofer; Rick Gelhausen; Jens Georg; Steffen Heyne; Michael Hiller; Kousik Kundu; Robert Kleinkauf; Steffen C Lott; Mostafa M Mohamed; Alexander Mattheis; Milad Miladi; Andreas S Richter; Sebastian Will; Joachim Wolff; Patrick R Wright; Rolf Backofen
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

Review 3.  Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria.

Authors:  Marta Robledo; Natalia I García-Tomsig; José I Jiménez-Zurdo
Journal:  Microorganisms       Date:  2020-03-10

4.  The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment.

Authors:  Martin Raden; Teresa Müller; Stefan Mautner; Rick Gelhausen; Rolf Backofen
Journal:  BMC Bioinformatics       Date:  2020-01-13       Impact factor: 3.169

5.  GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs.

Authors:  Richard A Schäfer; Steffen C Lott; Jens Georg; Björn A Grüning; Wolfgang R Hess; Björn Voß
Journal:  Bioinformatics       Date:  2020-08-01       Impact factor: 6.937

6.  CopomuS-Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments.

Authors:  Martin Raden; Fabio Gutmann; Michael Uhl; Rolf Backofen
Journal:  Int J Mol Sci       Date:  2020-05-28       Impact factor: 5.923

7.  An Integrated Database of Small RNAs and Their Interplay With Transcriptional Gene Regulatory Networks in Corynebacteria.

Authors:  Mariana Teixeira Dornelles Parise; Doglas Parise; Flavia Figueira Aburjaile; Anne Cybelle Pinto Gomide; Rodrigo Bentes Kato; Martin Raden; Rolf Backofen; Vasco Ariston de Carvalho Azevedo; Jan Baumbach
Journal:  Front Microbiol       Date:  2021-06-17       Impact factor: 5.640
  7 in total

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