Annotation and Analysis of Gene Families in Glycine max using DNA Subway

The complete soybean genome was sequenced and published in January 2010.  Soybean is estimated to have more than 48,000 protein coding loci belonging to about 9000 gene families ranging in size from 2 to over 300 members.  In addition, NCBI has accumulated nearly 1.5 million EST sequences for soybean.  We have designed research projects using DNA Subway and a few other publicly available bioinformatics tools that allow undergraduate majors in biology or computer science to characterize their own gene family.  Students identify all members of the family in soybean, search the Glycine max dbEST, assign ESTs to family members, and use DNA Subway to build models of each family member.  They are also able to identify orthologs in other plant species, build phylogenies, as well as identify potential conserved sequence domains to potentially provide clues to protein function. Other characterization studies carried out by some students include promoter element searches and in silico expression analysis using the EST metadata.  Projects are designed to be flexible in scope depending on the student’s ability and the features of the gene family as they emerge during the project.  Students are guided through projects with directed questions that allow hypothesis driven investigation.