genomics (bio 426) james madison university. why are you here? have you taught genomics before? plan...
TRANSCRIPT
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