DNA Builder: A Program to Design Oligonucleotides for the PCR Assembly of DNA Fragments
(Reference Number: UTSD:0993)

The software program is designed to assemble DNA fragments from synthetic oligonucleotides -- a powerful approach for creating virtually any DNA sequence in vitro.  It takes either DNA or protein sequence and automatically redesigns a new DNA sequence containing optimal/biased codons without alteration of the protein sequence.  It can create or delete user-defined restriction sites as well.  The newly designed DNA sequence is then used to create a series of overlapping oligonucleotides.  The program automatically checks the set of oligonucleotides for any undesired homology amongst them (hairpins,etc).  Assembly problems predicted by the program are remedied automatically by reiteratively substituting alternate codons until an acceptable design is found.  The final output is a list of oligonucleotides sequences that can be submitted to a DNA synthesizer.  It operates under Windows or Macintosh.