RNAthermsw: direct temperature simulations for predicting the location of RNA thermometers.
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.
Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel.
Alexander
A
Churkin
Microsoft Research Israel, Herzliya, Israel.
Assaf
A
Avihoo
Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel.
Michal
M
Shapira
Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel.
Danny
D
Barash
D000818:Animals; D003198:Computer Simulation; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D004926:Escherichia coli; D029968:Escherichia coli Proteins / Q000378:metabolism; D050957:HSP110 Heat-Shock Proteins / Q000235:genetics; D018840:HSP70 Heat-Shock Proteins / Q000235:genetics; D006360:Heat-Shock Proteins / Q000378:metabolism; D018869:Heat-Shock Response; D006801:Humans; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012984:Software; D013696:Temperature; D013821:Thermometers
D029721:Drosophila Proteins; D029968:Escherichia coli Proteins; D050957:HSP110 Heat-Shock Proteins; D018840:HSP70 Heat-Shock Proteins; C121993:HSPA4 protein, human; D006360:Heat-Shock Proteins; C544596:Hsp70Aa protein, Drosophila; C097578:IbpA protein, E coli; D012313:RNA