Genomics (BIO 426) James Madison University. Why are you here? Have you taught Genomics before? Plan to teach it soon? Might you teach it sometime? Just.

Genomics (BIO 426)James Madison University

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?

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

Genomics (BIO 426)James Madison University

Jr/Sr-level lab course, 17 students

4-credits, semesterTwo 3-hour periods per weekFormat: mixed lecture / discussion / project / lab

Text - Bioinformatics by Baxevanis and Ouellette Readings - from the primary literatureLab - cloned and partially sequenced a viral genomeProjects - protein families, genomes

Outline for workshop

Background LearningDiscussion

Protein Family ProjectExercise I - structure/alignmentDiscussion

Laboratory ProjectExercise II - Sequence analysisDiscussion

Background Learning

Cold Spring Harbor TAGC, Nov 2005

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

Background Learning

Course website

Readings, discussions

http://csm.jmu.edu/biology/monroejd/genomics/genomics.html

Background Learning

Course website

Readings, discussions

In-class exercises1. Analyzing 35S sequencing gels by hand

Background Learning

Course website

Readings, discussions

In-class exercises1. Analyzing 35S sequencing gels by hand

2. Crepe paper cloning

Background Learning

Course website

Readings, discussions

In-class exercises1. Analyzing S35 sequencing gels by hand

2. Crepe paper cloning

Debate on sequencing strategies

Web-based exercises (tutorials)

1. Exploring sequence databases

2. Repetitive DNA and Sequencing Genomes

3. Finding genes in raw genomic DNA sequence

3. E-values (Ex4.doc)

4. Using BLAST to identify protein sequences

5. Multiple Sequence Alignment using ClustalW

6. Introduction to Artemis

Whole genome research project Purpose Process Outcome

Break for questions and comments

Outline for workshop

Background LearningDiscussion

Protein Family ProjectExercise I - structure/alignmentDiscussion

Laboratory ProjectExercise II - Sequence analysisDiscussion

• Each student was assigned a protein family

• Start with 3D structure (Cn3D)

• Find homologs (paralogs and orthologs), alignand 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

Protein Family Project -

protein structure

sequence

paralogs orthologs

literature

alignments

trees

Cn3D

BLAST

ClustalWBoxShade

TreeView

Protein Family Project -

Students wrote papers and gave 10-min Powerpoint presentations

Exercise I - structure/alignment

Discussion

Outline for workshop

Background LearningDiscussion

Protein Family ProjectExercise I - structure/alignmentDiscussion

Laboratory ProjectExercise II - Sequence analysisDiscussion

Laboratory Project: Learning by DoingSequencing 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

Laboratory Project

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

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 topoisomerasePhage tail fiber

Exercise II - Sequence analysis

Discussion