RNAthermsw: Direct temperature simulations for predicting the location of RNA thermometers

Alexander Churkin; Assaf Avihoo; Michal Shapira; Danny Barash

doi:10.1371/journal.pone.0094340

RNAthermsw: Direct temperature simulations for predicting the location of RNA thermometers

Alexander Churkin, Assaf Avihoo, Michal Shapira, Danny Barash

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

Abstract

The mechanism of RNA thermometers is a subject of growing interest. Also known as RNA thermosensors, these temperature-sensitive segments of the mRNA regulate gene expression by changing their secondary structure in response to temperature fluctuations. The detection of RNA thermometers in various genes of interest is valuable as it could lead to the discovery of new thermometers participating in fundamental processes such as preferential translation during heat-shock. RNAthermsw is a user-friendly webserver for predicting the location of RNA thermometers using direct temperature simulations. It operates by analyzing dotted figures generated as a result of a moving window that performs successive energy minimization folding predictions. Inputs include the RNA sequence, window size, and desired temperature change. RNAthermsw can be freely accessed at http://www.cs.bgu.ac.il/~rnathemsw/RNAthemsw/ (with the slash sign at the end). The website contains a help page with explanations regarding the exact usage.

Original language	English
Article number	e94340
Journal	PLoS ONE
Volume	9
Issue number	4
DOIs	https://doi.org/10.1371/journal.pone.0094340
State	Published - 9 Apr 2014

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences
General

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RNAthermsw: Direct temperature simulations for predicting the location of RNA thermometers

Abstract

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