Bioinformatics Workshop Gives Young Scientists ‘Hands-On’ Experience

Three-day ‘jamboree’ hosted by The College of Wooster with support from HHMI

WOOSTER, Ohio — While few outside the field of genomics science might characterize a bioinformatics workshop as a “jamboree,” those who attended the three-day event at The College of Wooster earlier this month, would likely agree that despite the complex subject matter there was a festive-like atmosphere of discovery at each of the sessions.

Dean Fraga, a professor of biology and biochemistry/molecular biology at Wooster, organized the workshop to give graduate and undergraduate students in northeast Ohio an opportunity to learn more about mapping and analyzing DNA and protein sequences.

“We have held similar events in the past, including an annotation session for Paramecium that drew an international crowd several years ago,” said Fraga. “This one focused on the local community, and judging from the response, there was a real need in this area.”

Approximately 40 students from such schools as Wooster, Ashland, Miami, and Kent State, as well as the Ohio Agricultural Research and Development Center (OARDC), signed up to learn more about this burgeoning field, including Hunter Vanhorn, a rising sophomore at Wooster where he is majoring in biochemistry and molecular biology. “It sounded very useful, so I thought I would check it out,” he said. “I’m looking into (a possible career in) biotechnology, and there are a lot of software programs that I never heard of. Plus, it was free.”

A collaboration between the Howard Hughes Medical Institute and The College of Wooster enabled Fraga to offer the workshop at no charge as a “goodwill gesture” to young scientists.

Also taking advantage were Shane Bemiller, a biology major from Ashland University, who said it gave him “additional tools to expand the breadth of his research,” and Emily Boyd, a biology major from Indiana Wesleyan University, who described it as “a really good way to learn about bioinformatics while doing an internship at OARDC.”

Daniel Thomas, a first-year graduate student at OARDC, also found the workshop useful. “I came to gain more hands-on experience in bioinformatics,” he said. “The practical experience in using alignment tools and finding motifs in a DNA sequence was really helpful.”

The workshop began with an introduction to the National Center for Biotechnology Information website and a focus on how to extract information as well as how to use the tools available to refine searches or to conduct additional analyses or comparisons. The second day featured motif-finding, using tools that could identify signature sequences in DNA (such as promoter or enhancer elements) or in protein sequences (such a signal tags). The third day was devoted to molecular evolution topics and how to use some readily available online tools to do alignments, construct phylogenetic trees, and test for selection on individual sequences.

Guest speakers included Sofia Visa of The College of Wooster, who spoke at the opening session about the nature of biological databases; Mason Posner of Ashland University, who talked about motif finding; Bill Morgan of Wooster, who discussed a case study on motifs; Brian McSpadden-Garnder of the OARDC, who explained how to annotate a genome; Andrew Kiss of Miami University, who covered the topic of phylogenetics; and Fraga, who described multiple-sequence alignments.

“The workshop provided hands-on experience with various software and web-based tools,” said Fraga. “It also went on to explain how to use those tools to generate hypotheses, which I think everyone found very valuable.”