Genomics (BIO 426) James Madison University

1. Genomics (BIO 426) James Madison University

2. Why are you here? Have you taught Genomics before? Plan to teach it soon? Might you teach it sometime? Just curious? Nowhere else to be right now?

3. Why are we here? Co-taught Genomics Spring ‘06 Louise Temple - Microbiologist sequenced Bordetella avium genome Jon Monroe - Plant Molecular Biologist sequenced several Arabidopsis genes

4. Genomics (BIO 426) James Madison University Jr/Sr-level lab course, 17 students 4-credits, semester Two 3-hour periods per week Format: mixed lecture / discussion / project / lab Text - Bioinformatics by Baxevanis and Ouellette Readings - from the primary literature Lab - cloned and partially sequenced a viral genome Projects - protein families, genomes

5. Outline for workshop • Background Learning • Discussion • Protein Family Project • Exercise I - structure/alignment • Discussion • Laboratory Project • Exercise II -Sequence analysis • Discussion

6. Background Learning Cold Spring Harbor TAGC, Nov 2005

7. Background Learning Cold Spring Harbor TAGC, Nov 2005 * Sequence Formats * Pairwise Comparisons * Multiple Sequence Alignments * Gene Prediction * Sequence Variation * Genome Analysis * Protein Structure * Proteomics * Phylogenetics

8. Background Learning Course website http://csm.jmu.edu/biology/monroejd/genomics/genomics.html Readings, discussions

9. Background Learning Course website Readings, discussions In-class exercises 1. Analyzing 35S sequencing gels by hand

10. Background Learning Course website Readings, discussions In-class exercises 1. Analyzing 35S sequencing gels by hand 2. Crepe paper cloning

11. Background Learning Course website Readings, discussions In-class exercises 1. Analyzing S35 sequencing gels by hand 2. Crepe paper cloning Debate on sequencing strategies

12. Web-based exercises (tutorials) • Exploring sequence databases • Repetitive DNA and Sequencing Genomes • Finding genes in raw genomic DNA sequence • E-values (Ex4.doc) • Using BLAST to identify protein sequences • Multiple Sequence Alignment using ClustalW • Introduction to Artemis

13. Whole genome research project Purpose Process Outcome

14. Break for questions and comments

15. Outline for workshop • Background Learning • Discussion • Protein Family Project • Exercise I - structure/alignment • Discussion • Laboratory Project • Exercise II -Sequence analysis • Discussion

16. Protein Family Project - • Each student was assigned a protein family • Start with 3D structure (Cn3D) • Find homologs (paralogs and orthologs), align and build trees • Learning goals - • Link conserved and nonconserved residues from alignment with 3D structure • Use orthologs to see common features • Use paralogs to see unique features

17. protein structure Cn3D literature sequence BLAST paralogs orthologs ClustalW BoxShade alignments TreeView trees

18. Protein Family Project - Students wrote papers and gave 10-min Powerpoint presentations

19. Exercise I - structure/alignment Discussion

20. Outline for workshop • Background Learning • Discussion • Protein Family Project • Exercise I - structure/alignment • Discussion • Laboratory Project • Exercise II -Sequence analysis • Discussion

21. Laboratory Project: Learning by Doing Sequencing a viral genome Bacteriophage infecting Bordetella avium Isolated phage DNA Sheared and restriction digested the DNA Cloned fragments into pBluescript Sequenced ~500 clones through VCU Analyzed the sequence - Artemis and Sequencher

22. Laboratory Project

23. Accomplishments: Clones sequenced: ~500, Forward and Reverse ~80% had inserts Number of contigs: ~80, ranging from 2500 to 200 bases Number of genes identified: ~10 highly likely phage genes

24. Accomplishments: Clones sequenced: ~500, Forward and Reverse ~80% had inserts Number of contigs: ~80, ranging from 2500 to 200 bases Number of genes identified: ~10 highly likely phage genes e.g., DNA topoisomerase Phage tail fiber

25. Exercise II - Sequence analysis • Discussion