Genomics (BIO 426)

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Genomics (BIO 426) James Madison University
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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?
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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
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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
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Outline for workshop Background
Learning Discussion Protein Family
Project Exercise I - structure/alignment Discussio
n Laboratory Project Exercise II - Sequence
analysis Discussion
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Background Learning Cold Spring Harbor TAGC, Nov
2005
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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
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Background Learning Course website
http//csm.jmu.edu/biology/monroejd/genomics/genom
ics.html
Readings, discussions
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Background Learning Course website
Readings, discussions
In-class exercises 1. Analyzing 35S sequencing
gels by hand
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Background Learning Course website Readings,
discussions In-class exercises 1. Analyzing 35S
sequencing gels by hand 2. Crepe paper
cloning
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Background Learning Course website Readings,
discussions In-class exercises 1. Analyzing S35
sequencing gels by hand 2. Crepe paper
cloning Debate on sequencing strategies
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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

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Whole genome research project Purpose
Process Outcome
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Break for questions and comments
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Outline for workshop Background
Learning Discussion Protein Family
Project Exercise I - structure/alignment Discussio
n Laboratory Project Exercise II - Sequence
analysis Discussion
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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

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protein structure
Cn3D
sequence
literature
BLAST
paralogs
orthologs
ClustalW BoxShade
alignments
TreeView
trees
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Protein Family Project - Students wrote papers
and gave 10-min Powerpoint presentations
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Exercise I - structure/alignment Discussion
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Outline for workshop Background
Learning Discussion Protein Family
Project Exercise I - structure/alignment Discussio
n Laboratory Project Exercise II - Sequence
analysis Discussion
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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
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Laboratory Project
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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
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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
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Exercise II - Sequence analysis Discussion