Database of standard biological parts derived from plasmid features


GenoLIB: a database of biological parts derived from a library of common plasmid features


Neil R. Adames Mandy L. Wilson Gang Fang Matthew W. Lux Benjamin S. Glick Jean Peccoud


Published in: Nucleic Acids Research
Volume: 43, Issue: 10, Pages: 4823-4832
Published: 05/26/2015
DOI: 10.1093/nar/gkv272

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Our Discussion:

Synthetic biologists rely on databases of standard biological parts to design genetic devices and systems. The Registry of Standard Biological Parts and other community resources provide the sequences and descriptions of thousands of genetic parts. The content of these database  is often derived from features of previously described plasmids using ad hoc, error-prone and time-consuming curation processes. Existing databases of plasmids and features are loosely organized, making their curation difficult. They often lack consistency in the way they identify and describe sequences. Furthermore, legacy bioinformatics file formats like GenBank do not provide enough information about the purpose of features. We have analyzed the annotations of a library of ∼2000 widely used plasmids to build a non-redundant database of plasmid features. We looked at the variability of plasmid features, their usage statistics and their distributions by feature type. We segmented the plasmid features by expression hosts. We derived a library of biological parts from the database of plasmid features. The library was formatted using the Synthetic Biology Open Language, an emerging standard developed to better organize libraries of genetic parts to facilitate synthetic biology workflows. The library was converted into GenoCAD grammar files. Users can import the file to design new plasmids using standard biological parts.


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