DegenPrimer is a tool to check the quality of degenerate primers. It calculates melting temperatures, finds stable dimers, hairpins and crossdimers, uses BLAST search and full-fledged PCR simulation cycle by cycle to provide accurate predictions of possible PCR products and their quantities.
All calculations of thermodynamic parameters are made using Nearest Neighbor model and the latest thermodynamic tables with corrections for particular PCR conditions. PCR simulation supports multiplex PCR.
The program has simple command line interface as well as a GUI (which is a separate package: https:/
Dependecies: python2 >= 2.7,
SciPy >= 0.9
View full history Series and milestones
trunk series is the current focus of development.