Registered 2012-06-28 by Allis Tauri

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://launchpad.net/degenprimergui). PBS is also supported with PBS-utils package at PyPi (https://pypi.python.org/pypi/PBS-utils)

Dependecies: python2 >= 2.7,
             Biopython >= 1.58,
             SciPy >= 0.9

PPA: https://launchpad.net/~allista/+archive/ppa

Project information

Maintainer:
Allis Tauri
Driver:
Allis Tauri
Licence:
GNU GPL v3

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Programming languages:
python

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Latest version is 2.8
released on 2014-03-29

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