A genetic parts library published in Nucleic Acids Research

Genetic parts library derived from common plasmid features

A quality genetic parts library is key to the success of any synthetic biology project. Jean Peccoud, GenoFAB’s founder, and his colleagues at the Virginia Bioinformatics Institute published a paper in Nucleic Acids Research that highlights the power of the GenoCAD DNA design software. Titled “GenoLIB: a database of biological parts derived from a library of common plasmid features,” the paper describes the extraction of specific genetic parts from over 1700 DNA sequences and plasmids.

A key problem described by the authors is the lack of consistent sequence information for various plasmids and DNA constructs. While there are efforts to standardize this information and provide full DNA sequences for genetic constructs, many groups and databases still use their own system. Peccoud’s team used resources from SnapGene, which include a well-curated database, to export a list of plasmids and individual feature sequences. Using a custom-built database and analysis tool, the team aligned and analyzed the > 1700 DNA sequences. Discrete features (DNA parts) were extracted from these plasmids, which had been organized by host organism. After additional curation to remove duplicate features, the team assessed how often the various DNA parts were used in different plasmids.

Additionally, they looked at variants of the same features. This latter step is extremely valuable for synthetic biology and DNA design projects, as it allows for flexible design. In GenoCAD, we think of parts-based design in terms of language. The specific DNA parts are “words,” a plasmid or complex DNA construct is the “book,” and the rules dictating its construction is the grammar. Thinking about it in those terms, having multiple variants of the same part is like using a synonym in a sentence, changing the words but maintaining the meaning.

Using GenoCAD to distribute the GenoLIB genetic parts library

Ultimately, Peccoud and his group took the newly annotated list of parts, now called GenoLIB, and created a GenoCAD grammar out of it. This included describing the relationships between parts and organizing them based on category. Because the new grammar is available in the GenoCAD DNA design software, it will benefit users of the platform by providing them with a huge number of parts that can be incorporated into new complex constructs.

Derive your own genetic parts library from GenoLIB

If you have questions about how GenoLIB might be able to help you, or about how you can create your own parts and grammars in GenoCAD, open a ticket by going to our support page.