1. Using DNA Subway in the Classroom Genome Annotation: Red Line

2. DNA Subway is a suite of bioinformatics tools which have been placed in simplified workflows. These tools allow students to work with the same data (DNA or Protein sequence data) used by biologists. The DNA Subway can be used in the classroom to illustrate the basic principles of molecular biology. Once students have mastered the biological concepts and become familiar with the bioinformatic tools, they can continue to use DNA subway to examine new data, which can result in novel findings. DNA Subway Lesson Sketch

3. For each concept you can create 3-4 step lesson plan 1.Choose a concept that can be illustrated in terms of genomic biology (e.g. “genes are spliced”). 2.Select (or have students research) a real example of a gene that may/may not be an example of the concept. 3.Use DNA subway to confirm your hypothesis 4.If possible do a “real world” in vivo experiment to demonstrate the concept. DNA Subway Lesson Sketch

4. It is not surprising that many students have difficulty expressing a tractable definition of what a gene is given that the science of genomics recently outpaces the adoption of new textbooks. Nice bits of trivia, but maybe not immediately useful for students! DNA Subway What is a gene?

5. Concept: Many genes are spliced Example: Jasmonate signaling In silico discovery 1: discover splicing In silico discovery 2: discover alternative splicing In vitro: sequence spliceforms In vivo: Analyze plants DNA Subway What is gene splicing?

6. Using the Red Line, you can create a lesson plan that address several objectives What a gene is and how it relates to DNA What are the components of genes Dogma of molecular biology; DNA – RNA – Protein How genes can “code for” proteins How statistical models (“mathematical evidence”) to predict genes How biological evidence (cDNAs, EST, etc.) can confirm predictions DNA Subway Gene annotation with Red Line

7. Annotations are descriptions of features of the genome Structural: exons, introns, UTRs, splice forms etc. Coding & non-coding genes Expression, repeats, transposons Annotations should include evidence trail Assists in quality control of genome annotations Examples of evidence supporting a structural annotation: Ab initio gene predictions ESTs Protein homology DNA Subway What are annotations?

8. Protein Domains InterPro Scan: combines many HMM databases GO and other ontologies Pathway mapping E.g. BioCyc Pathway tools DNA Subway What are annotations?

9. DNA Subway Workflow options Yandell & Ence. Nature Reviews Genetics 13, 329-342 (May 2012) | doi:10.1038/nrg3174

10. First, use DNA subway to show how we can reveal features of a sequence. Create a project using a sample sequence. Once students have mastery, they can come back and create their own projects using real data. DNA Subway Gene annotation with Red Line

11. Using the synthetic contig as our example, take students through project creation and run repeat masker and on of the gene prediction algorithms ( Augusts and FGenesH) then open Apollo. DNA Subway Gene annotation with Red Line

12. In stepwise fashion, you can use the synthetic contig in Apollo to introduce the following component concepts introns and exonsstart and stop codons DNA Subway Gene annotation with Red Line

13. Add components of evidence, you can discuss how these predictions are made biological evidence Codons, UTRs, reading frames, splicing DNA Subway Gene annotation with Red Line

14. Use PCR mutagenesis to add/delete codons DNA Subway Gene annotation with Red Line – Confirming with experimentation