BIOINFORMATICS

UNAFold

8 December 2010

Integrated DNA Technologies

Integrated DNA Technologies (IDT) and Rensselaer Polytechnic Institute (RPI) have launched the UNAFold secondary structure prediction software. The software will be used to more accurately detect secondary structures within sequences submitted by customers and will be available through a web-based interface on IDT’s SciTools website.

UNAFold is a software package for nucleic acid folding and hybridisation prediction. Folding of single-stranded RNA or DNA, or hybridisation between two single strands, is accomplished in a number of ways. Partition functions can be computed to derive base pair probabilities and stochastic samples of foldings or hybridisations. Energy minimisation methods compute minimum free energy foldings or hybridisations, and can also compute suboptimal foldings that mimic the performance of the mfold software. The UNAFold software powers the DINAMelt web server that has been running at Rensselaer since 2005.

For melting simulations, the package computes not just melting temperatures, but entire melting profiles. UV absorbance at 260nm, heat capacity change (Cp), and mole fractions of different molecular species are computed as a function of temperature. ITC (Isothermal Titration Calorimetry) and van ’t Hoff plots are also simulated.

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