DNA Subway – An Educational Bioinformatics Platform for Gene and Genome Analysis: DNA Barcoding, and RNA-Seq

Abstract Text: DNA Subway is an educational bioinformatics platform developed by the iPlant Collaborative (NSF #DBI–0735191). DNA Subway bundles research-grade bioinformatics tools, high-performance computing, and databases into workflows with an easy-to-use interface. “Riding” DNA Subway lines, students can predict and annotate genes in up to 150kb of DNA (Red Line), identify homologs in sequenced genomes (Yellow Line), identify species using DNA barcodes and phylogenetic trees (Blue Line), and examine RNA-Seq datasets for differential transcript abundance (Green Line). With support for plant and animal genomes, DNA Subway engages students in their own learning, bringing to life key concepts in molecular biology and genetics. DNA barcoding and RNA extraction wet-lab experiments support a variety of inquiry-based learning experiences using student-generated data. Products of student research can be exported, published, and utilized in follow-up experiments. DNA Subway is freely accessible online at dnasubway.iplantcollaborative.org.

Keywords: DNA Barcoding, RNA-Seq, Undergraduate Education