What is GenoCAD™?

Chemical synthesis of custom DNA made on order calls for software streamlining the design of synthetic DNA sequences. GenoCAD can be used to design protein expression vectors, artificial gene networks, and other genetic constructs composed of multiple functional blocks called genetic parts. By capturing design strategies in grammatical models of DNA sequences, GenoCAD guides the user through the design process. By successively clicking on icons representing structural features or actual genetic parts, complex constructs composed of dozens of functional blocks can be designed in a matter of minutes. GenoCAD automatically derives the construct sequence from its comprehensive libraries of genetic parts. Upon completion of the design process, users can download the sequence for synthesis or further analysis. GenoCAD users who elect to create a personal account on the system can customize their workspace by creating their own parts libraries, adding new parts to the libraries, or reusing designs to quickly generate sets of related constructs.

Getting started

• Step by step tutorial. http://www.genocad.org/tutorial.pdf
• Technical support: http://sourceforge.net/projects/genocad/support

Who develops GenoCAD?

GenoCAD is developed by the Virginia Bioinformatics Institute. More information about Jean Peccoud's research group.

This material is based upon work supported by the National Science Foundation under Grant No. EF-0850100. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Advisory Board

GenoCAD benefits from the guidance of an External Advisory Board comprised of the following scientists:

• Chris Anderson, University of California Berkeley
• Brian Bramlett, Lux Bio Group
• Malcolm Campbell, Davidson College
• Jacques Cohen, Brandeis University
• Otto Folkerts, Chromatin, Inc.
• Claes Gustafsson, DNA2.0
• Sara Klucking, Department of Homeland Security
• Ron Weiss, Massachusetts Institute of Technology

References

• Cai Y, Hartnett B, Gustafsson C, Peccoud J (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23(20): 2760-2767.

• Peccoud J, Blauvelt MF, Cai Y, Cooper KL, Crasta O, DeLalla EC, Evans C, Folkerts O, Lyons BM, Mane SP, Shelton R, Sweede MA, Waldon SA. (2008) Targeted development of registries of biological parts PLoS ONE 3(7):e2671.

• Goler JA, Bramlett BW, Peccoud J. (2008) Genetic design: rising above the sequence. Trends in Biotechnology 26(10):538-44.

• Czar MJ, Anderson JC, Bader JS, Peccoud J. (2009) Gene synthesis demystified. Trends in Biotechnology 27(2):63-72.

• Czar MJ, Cai Y, Peccoud J. (2009) Writing DNA with GenoCAD Nucleic Acids Research 37:W40-7.

• Cai Y, Lux MW, Adam L, Peccoud J. (2009) Modeling structure-function relationships in synthetic DNA sequences using attribute grammars PLoS Comput Biol 5(10):e1000529

• Cai Y, Wilson ML, Peccoud J. (2010) GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs Nucleic Acids Research 38, 2637-2644.

Technical support

Use the ticketing system available at https://sourceforge.net/projects/genocad/support to submit your technical support requests or suggest new features.

GenoCAD Source Code

GenoCAD is distributed open source using the Apache Version 2.0 License. This license has been approved by the Open Source Initiative.

The GenoCAD source code is hosted on SourceForge https://sourceforge.net/projects/genocad/develop.