GenomeDesign: A Bioinformatics Program for Genome and Multiplex Gene Synthesis

Herein we present a computer program to analyze the complexity of genomes for de novo genome synthesis. The program combines several open source bioinformatics software to predict tandem repeats, hairpin loops, DNA similarity, and the possibility of DNA mis-pairing. In addition, the program automatically divides the genome sequence into unique DNA groups and segments based on the user-specified input parameters and dynamically optimizes the members of group DNA segments to achieve unique and uniform enzymatic DNA assembly. The output reports the complexity of the target genome, the DNA segments, the oligonucleotide sets, and the recommended assembly conditions for genome synthesis. The calculation time and performance of this software have been demonstrated on five genomes (10.3 kbp 5.5 Mbp) for human immunodeficiency virus, herpesvirus, Mycoplasma genitalium, Mycoplasma capricolum, and E. coli. To our knowledge, GenomeDesign is the first bioinformatics program capable of facilitating genome design.