Ensemble_Calc | Tool name | Ensemble_Calc |
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| URL | 1. http://mfold.rna.albany.edu/?q=DINAMelt/Ensemble-calc 2. http://mfold.rna.albany.edu/Ensemble |
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| Important features | Assists in predicting the occurrence of microRNA:mRNA interaction at specified concentrations by computing the final concentrations of microRNA and mRNA and the net free energy change of interaction. |
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| Citations | Ragan C, Zuker M, Ragan MA. Quantitative prediction of miRNA-mRNA interaction
based on equilibrium concentrations. PLoS Comput Biol. 2011 Feb;7(2):e1001090.
Epub 2011 Feb 24. PubMed PMID: 21390282; PubMed Central PMCID: PMC3044769.
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| Year of publication | 2011 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | EXPERIMENTAL data analysis, EXPERIMENTAL aids; predicting mRNA-microRNA interaction, 1. http://mfold.rna.albany.edu/?q=DINAMelt/Ensemble-calc 2. http://mfold.rna.albany.edu/Ensemble, Assists in predicting the occurrence of microRNA:mRNA interaction at specified concentrations by computing the final concentrations of microRNA and mRNA and the net free energy change of interaction. , Ragan C- Zuker M- Ragan MA. Quantitative prediction of miRNA-mRNA interaction
based on equilibrium concentrations. PLoS Comput Biol. 2011 Feb;7(2):e1001090.
Epub 2011 Feb 24. PubMed PMID: 21390282; PubMed Central PMCID: PMC3044769.
, 2011, 100, Online/ downloadable , I. QUERY OR INPUT DATA:
1. Input free energy of a. hybridization of the oligonucleotide to the target b. the folded oligonucleotide (generally zero- since a short oligo does not usually fold) c. the folded target d. the folded target with the hybridization site restricted to be single-stranded 2. Type the total strand concentration of a. the oligo (Default: 1000 nM = 1 μM) b. the target (Default: 1000 nM = 1 μM.) 3. Choose the concentration units (nM- μM- mM) 4. Type the the temperature (deg C):
II. OUTPUT DATA: Details on quantitative estimation of microRNA-mRNA interaction III. ADDITIONAL INFORMATION: The authors have compared their predictions to experimentally confirmed microRNA-mRNA interactions (and non-interactions) in Drosophila melanogaster and in human., Analyze microRNAs related to chicken. |
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