New Software to Accurately Detect Secondary Structures within Sequences

Integrated DNA Technologies (IDT) announces the launch of the UNAFold secondary structure prediction software at IDT. The software will be used to more accurately detect secondary structures within sequences submitted by customers, and will be made freely available through a web-based interface on IDT’s SciTools™ website.

“We’re excited about the improved fidelity of this software and the positive impact it should have on our customers” commented Robert Dawson, Director of Bioinformatics for IDT. “Not only are we better able to help customers order more effective sequences, but we’re able to open the software up for them to use without having to order”. Michael Zuker of Ressselaer said “I’m delighted to receive such an enthusiastic endorsement from a company that is so well known and respected worldwide. Anyone I talk to who is doing research in DNA orders their oligos or more specialized products from IDT.”

UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction. The name is derived from "Unified Nucleic Acid Folding and hybridization package". Folding of single-stranded RNA or DNA, or hybridization between two single strands, is accomplished in a variety of ways. Partition functions can be computed to derive base pair probabilities and stochastic samples of foldings or hybridizations. Energy minimization methods compute minimum free energy foldings or hybridizations, and can also compute suboptimal foldings that mimic the performance of the famous 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 260 nm, 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.

UNAFold may be downloaded freely for academic and other non-commercial use. Commercial use requires a special license from RPI. Follow the Company article page top right to download this software for free.