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Unified Nucleic Acids Folding Hybridization Prediction Simulator Software Program
Rensselaer Polytechnic Institute
posted on 07/23/2008
Highly acclaimed integrated collection of software programs that predicts folding for single-stranded RNA or DNA through combination of free energy minimization, parttion function calculations and stochastic sampling. Computes entire melting profile for melting simulations.
Suggested Uses
Nucleic acids calculations used for hybridizations and amplifications in:
- Life science research
- Drug development and discovery
- Diagnostics
Advantages
Benefits
- Cost Beneficial-Provides many applications in one package in an easy, user friendly manner
- Added special plug-in “OligoArrayAux”-accomodating calculations for oligo-arrays
Advantages
- The only program available that contains a unique ad hoc rule to correct for internal-free energy changes in unfolded, single-stranded molecules caused by base stacking
- The two interacting molecules are not required to be perfectly complementary or to be related at all
- User is not expected to provide hybridization; UNAfold computes minimal energies and partition functions over all possible hybridizations
- Entire melting profiles are computed as a function of temperature
- Allow for changes in mono-, and divalent cation conventrations
- The concentration of each complementary strand do not have to be the same allowing molecular beacon simulation versus target interactions
Detailed Description
Based on the famous “mfold”, the UNAFold software package is an integrated collection of programs that simulate nucleic acid folding and hybridization and its melting pathways for one or two single-stranded sequences. The package predicts folding for single-stranded RNA or DNA through combination of free energy minimization, partition function calculations and stochastic sampling.
For melting simulations, the package computes entire melting profiles, not just melting temperatures. UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of different molecular species are computed as a function of tempertaure.
The package runs and installs on all Unix and Linux platforms as well as on Mac OS X and Windows; XP and Vista. Images of secondary structures, hybridizations, and dot plots could be computed using common formats. Similarly, a variety of theorectically melting profile plots could be created or imported from real experimental results.
The package is “command line” driven. Underlying compiled programs may be used individually, or in special combinations through the use of a variety of Perl scripts. Users are encouraged to create their own scripts to supplement what comes with the package.
File Number: RPI UNAFOLD
Web site: http://www.rpitechnology.com
Other Information:
| Copyright: | Registered copyright TXu 1-173-513 |
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This innovation currently is not available for online licensing. Please contact Natasha Sanford at Rensselaer Polytechnic Institute for more information.
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