Creating a Microbial Genome Analysis Project using Publically Available Genome Sequences and Online Bioinformatics Programs
Tested Studies in Laboratory Teaching, 2016, Volume 37
Lori R. Scott, Todd C. Nickle, Stephen Koury, Brad Goodner, Katherine Houmeil, Ben McFarland, Jennifer Tenlen, Andrew Lumpe, Kimberly Murphy, D. Rhoads, D. Wood, & Daihong Chen
Abstract
The Department of Energy's Joint Genome Institute (DOE JGI) has sequenced the genomes of more than
200 microbes from across the Tree of Life as part of the Genome Encyclopedia of Bacteria and Archaea
(GEBA) project. The original GEBA project was completed in collaboration with the Leibniz-Institut
DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH). In the pilot study, the DOE
JGI sequenced 53 bacterial and three archaeal novel and highly diverse genomes, representing a first step
towards a phylogenetically balanced set of sequenced genomes across the microbial tree of life (Wu et al.,
2009). An additional approximately 200 GEBA genomes have since been sequenced (DOE JGI, 2015).
Most of these organisms are poorly represented in the scientific literature, thereby creating the opportunity
for undergraduate and high school students to make significant contributions to our understanding of
microbial genome structure and function. Students make these contributions by: 1) manually annotating open reading frames (ORFs) predicted by automated bioinformatics programs for the purpose of expanding
the original annotation and identifying errors; and/or 2) performing functional genomics studies to confirm the computer-based function predictions.
Keywords: bioinformatics, genomics, web-based
Boston University (2015)
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