Automatic oligonucleotide design for PCR-based gene synthesis

DNAWorks v3.2.3 David Hoover August 16, 2013

DNAWorks takes as input nucleotide and/or protein sequences, codon information, and other variables, and attempts to optimize a synthetic gene. It then outputs the gene with a variety of histograms and metrics for judging the probability of success for generating the gene by PCR. It also outputs the oligonucleotide sequences required for PCR synthesis of the synthetic gene.

This program is based on this publication:

Hoover DM, Lubkowski J. DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res. 2002 May 15;30(10):e43. PubMed PMID: 12000848; PubMed Central PMCID: PMC115297.

Kindly reference this publication if you use this for your work.

Currently, DNAWorks is written in Fortran. It will require a Fortran compiler.

There is a Makefile included with this repository, along with the require .f90 files. If you have gfortran available, then just type

make

and the dnaworks executable should compile.

Good luck!