Table 1.

Traversing the scientific process through student investigations within the GEP

The general process	The GEP process
1. Define the question	What genes or other features are present in this segment of a Drosophila species genome? What is the most likely gene structure? How has this region evolved?
2. Gather background information	D. melanogaster has been very well annotated; its evolutionary relationship with species under study allows for comparative analysis.
3. Experimental design	Students must decide which computational tools to use directly (e.g., BLAST to look for evidence of homology) and learn to seek other evidence from results displayed in a genome browser (e.g., ab initio gene predictors to look for computational evidence for the presence of a gene).
4. Collect experimental observations	Students generate BLAST results and collect other results (e.g., RNA-seq data) from a genome browser for their region of the genome.
5. Analyze collected data	Students create a gene model and test it using the collected observations; what gene model is best supported by the evidence?
6. Disseminate results	Students write papers and/or prepare talks or posters on their results, describing their results and defending their conclusions; pooled results are submitted to GenBank and linked to FlyBase.