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Using DNA Subway to Analyze Sequence Relationships

Author(s): Jason Williams1, Ray A. Enke2, Oliver Hyman2, Emily Lescak3, Sam S Donovan4, William Tapprich5, Elizabeth F Ryder6

1. DNA Learning Center 2. The Department of Biology, James Madison University; The Center for Genome & Metagenome Studies, James Madison University 3. University of Alaska 4. University of Pittsburgh 5. University of Nebraska-Omaha 6. Worcester Polytechnic Institute

1545 total view(s), 325 download(s)

Summary:

This is a bioinformatics exercise using the DNA Subway Blue Line, a user-friendly pipeline of bioinformatics tools, to analyze a collection of mosquito DNA bar-code sequences.

Licensed under CC Attribution-ShareAlike 4.0 International according to these terms

Version 2.0 - published on 30 May 2018 doi:10.25334/Q4J111 - cite this

Contents:

Description

These are instructions for a 120-minute bioinformatics lab in which students will learn how to use the DNA Subway (http://www.dnasubway.org) Blue Line. DNA Subway is an online educational bioinformatics platform. It bundles research-grade bioinformatics tools, high-performance computing, and databases into workflows with an easy-to-use interface. The Blue Line is a workflow for analyzing DNA bar-coding data to determine the taxonomic identity of an organism and examine inferred phylogenetic relationships among species. The data analyzed in this exercise is a collection of mosquito DNA sequences generated by students at James Madison University. Identification of a mosquito’s genus is important because different mosquitoes are capable of carrying different pathogens causing deadly human diseases.

Note: A natural way to divide this material may be to cover everything up to section IV (Phylogenetic Trees) in one class, leaving additional time to address trees in as much depth as desired.

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