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The NIDA/OTTC Plasmid Database: Developing a cost- and time-saving tool for archiving plasmid DNA

Monday, September 22, 2014 — Poster Session II

4:00 p.m. – 6:00 p.m.

FAES Academic Center




  • G Sun
  • R Domingo
  • W Lau
  • C Johnson
  • C Richie
  • B Harvey


A freely available plasmid database that is interoperable with popular freeware (such as a Plasmid Editor or ApE) is currently being developed for the NIDA Optogenetics and Transgenic Technology Core (OTTC). The plasmid database offers a versatile yet simple platform for scientists to store and analyze their plasmid data. Motivated by the need for a more comprehensive approach to archiving plasmid data, the database platform is enriched with numerous components beyond the repository, serving as an informatics platform designed to enhance the efficiency and analytic capabilities for scientists. The database provides informatics and visualization support for multiple plasmid upload scenarios. Uploading an unannotated plasmid sequence can yield a sequence alignment search against existing features in the database, allowing the user to validate from a list of candidate features. Annotations can also be performed in ApE and imported into the database, either individually or in bulk. A visualization component generates a dynamically drawn and intuitive map of a plasmid together with its features and annotations and allows users to visually compare two plasmids side-by-side. Collectively, the visualization and search functions of the database provide a time-saving tool for molecular biologists who want to catalog plasmids that are relevant to their laboratory.

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