Structure and Interaction Prediction in Prokaryotic RNA Biology

Overview

Journal Microbiol Spectr

Specialty Microbiology

Date 2018 Apr 21

PMID 29676245

Citations 8

Authors

Patrick R Wright

Martin Mann

Rolf Backofen

Affiliations

Soon will be listed here.

Abstract

Many years of research in RNA biology have soundly established the importance of RNA-based regulation far beyond most early traditional presumptions. Importantly, the advances in "wet" laboratory techniques have produced unprecedented amounts of data that require efficient and precise computational analysis schemes and algorithms. Hence, many methods that attempt topological and functional classification of novel putative RNA-based regulators are available. In this review, we technically outline thermodynamics-based standard RNA secondary structure and RNA-RNA interaction prediction approaches that have proven valuable to the RNA research community in the past and present. For these, we highlight their usability with a special focus on prokaryotic organisms and also briefly mention recent advances in whole-genome interactomics and how this may influence the field of predictive RNA research.

Citing Articles

A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.

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Interplay between Regulatory RNAs and Signal Transduction Systems during Bacterial Infection.

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

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Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions.

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

Raden M, Muller T, Mautner S, Gelhausen R, Backofen R BMC Bioinformatics. 2020; 21(1):15.

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