BLACKSBURG, Va., June 29, 2015 -- Virginia Tech scientists have released GenoLIB, a new database that allows synthetic biologists easy access to building blocks to engineer synthetic DNA molecules that meet user specifications. A new article in Nucleic Acids Research discusses the data release and its importance to the field.
Plasmids are engineered DNA molecules used to clone genes, produce biologic drugs, develop gene therapies, and many other applications in biotechnology and basic research. Peccoud’s group has analyzed the annotations of a collection of 2000 commonly-used plasmids, curated by GLS Biotech, LLC, a company that has developed an application called SnapGene.
To make the most useful and up-to-date database as possible, the team corrected a number of problems with existing annotations of plasmid sequences. The group also augmented the annotations by developing a system that builds on emerging standards like the Sequence Ontology and the Synthetic Biology Open Language.
“The development of a parts library is a painstaking effort that must take advantage of the annotations of thousands of plasmids that have been used by molecular biologists for decades,” said Jean Peccoud, professor at VBI. “The bioinformatic analysis of tens of thousands annotations has allowed us to greatly improve the quality and usability of the information in the database.”
In addition to providing building blocks to design new plasmids, GenoLIB provides reference sequences that can be used to revisit the annotation of existing plasmids available from different sources like Addgene and the Registry of Standard Biological Parts.
“At SnapGene we have invested years of effort developing a proprietary database of plasmid annotations and best-in-class software tools to allow biologists to better understand the sequences they work with,” said Benjamin Glick, SnapGene CEO. “Peccoud and his team have recognized the value of our curation effort and brought it to a new level by using informatics methods from synthetic biology.”
GenoLIB is available for non-commercial use in different formats from the online supplement of the article.
June 29, 2015