Bio343: Laboratory Methods In Genomics

Spring, 2011

A. Malcolm Campbell

Davidson students will be working NCSU and the David H. Murdock Research Institute to understand the blueberry (Vaccinium corymbosum) genome as a way to better understand the blueberry plant. The genome sequence has not been published and we will be among the first people in the world to see what the genome has to tell us.

Bio343 is a lab-only course that is primarily data analysis by computer. I am very excited about this course. Very few students in the world get to participate in genome annotation prior to publication. It will be a lot of fun to do real genomics research on a species which is poorly understood. The blueberrry is native to North American and holds many potentially beneficial compounds. Our task will be to reconstruct some of the metabolic pathways to see what metabolites we can predict would be produced in blueberries.

Tentative Syllabus: Bio 343 Laboratory Methods in Genomics
Office Hours: M & Tu: 3-4; Thurs: 2 - 3; or most anytime by appointment

Student Collaborators

Learning Outcomes

1) Understand what a gene is through in-depth analysis of a genome.

2) Describe how a eukaryotic genome is organized.

3) Categorize species-specific metabolic maps.

4) Evaluate automated annotation quality and accuracy.

5) Organize evolutionary paths as revealed in novel genomes.

6) Assess real genomics research process and all that comes with it.

7) Demonstrate computer skills used in modern genomics.

8) Perform collaborative learning and research.

9) Employ comparative genomics of plants to understand what constitutes a new species.


Required Readings

1) Online Tools (FireFox browser is best)

2) Research publications on genomes (PDFs distributed during semester).

Optional Readings

1) Genome: the autobiography of a species in 23 chromosomes. Matt Ridley. HarperCollins Publisher. Available at bookstores and

Tentative Weekly Schedule

Week of Semester
Subject Matter and Assignments Due
Week 1:
Jan 11 & 13

Discuss: semester-long research plans & set educational goals

Discuss: domains of life, genome sequencing, DHMRI and our species

Blueberry genome sequence home page

Blueberry genome portal

Wiki Online Glossary

Standard Operating Procedure (SOP), Quality Control (QC), and Triage

Amino Acids Table (memorize 1 letter code)

Genetic Code

Read the paper from first class: Bakke et al., 2009

Important background information:

  • Anthocyanins
  • Flavonoids
  • Stilbenes
  • 454 sequencing
  • Illumina sequencing
  • Blueberry phylogeny
  • Blueberry varieties
  • Blueberry wine
  • Wine and sucrose vs. fructose levels
  • pectins for making jam (starting place?)
  • Myb transcription factors
  • lignin
  • sucrose synthase
  • pH of blueberries
  • what rRNA genes?
  • RBS for eukaryotes?
  • How many chromosomes?
  • Eukaryotic ori??
  • alternative start codons in eukaryotes?
  • EST source?


Week 2:
Jan 18 & 20

Discuss fieldtrip on Thursday

8 reports on blueberries

Revise your reports in class

Fieldtrip to DHMRI: meet in Baker parking lot near vans no later than 9:30. Bring material for notes and a camera if you have one.

Read strawberry and grape genome papers (main text only for now)

Week 3:
Jan 25 & 27


Discuss strawberry and grape genome papers

Discuss blueberry grant proposal

Start to explore sequences with Apollo


Establish SOP (standard operating procedures) for genes.

Databases and Tools: BLAST, CDD, KEGG, BioCyc, Tcoffee, EC numbers, and phylogenetic trees, Rosaceae Genome Database, phytochemical database, and Apollo genome viewer


Work in groups to choose first research project - smaller scale

Week 4:
Feb 1 & 3

Finalize plan and begin project- smaller scale

Make clear the goals for each person

Controlled vocabulary

Problems to be addressed: Pseudogenes, transposons, horizontal gene transfer, orthologs, paralogs, homology, hypothetical genes, unknown function, quality of data for annotation.

See results from previous years

Distribute newest genome compilation.

Learn very basic UNIX commands.

Find orthologs in blueberry genome

1) make db (only have to do this once per computer)
w10120:Desktop macampbell$ /usr/local/ncbi/blast/bin/makeblastdb -title testdb -dbtype nucl -in bb_latest_assembly.fasta

2A) running BLAST
w10120:Desktop macampbell$ /usr/local/ncbi/blast/bin/blastn -query scf1453.fasta -db bb_latest_assembly.fasta -outfmt "7 qacc sacc evalue qstart qend sstart send"

2B) do this to see alignments (just leaving off the output changes from the first BLAST we learned)
w10120:Desktop macampbell$ /usr/local/ncbi/blast/bin/blastn -query scf1453.fasta -db bb_latest_assembly.fasta

3) To get blast help
change directory until you are inside bin
w10120:~ macampbell$ cd /usr/local/ncbi/blast/bin/

w10120:bin macampbell$ blastn -hlep

you might find it easier to type
/usr/local/ncbi/blast/bin/blastn -help
So you don't have to keep cd'ing in and out of the current folder.

What might be even more useful if you are fiddling with lots of options is
to type this:
/usr/local/ncbi/blast/bin/blastn -help > blastnhelp.txt

This will create a text file in your current folder (e.g. Desktop) with
the help in it, so you can have it open in another window while you are


Discuss end goals and methods for accomplishing this

Update class on progress so far

Week 5:
Feb 8 & 10

Continue projects

10 glossary entries for each student (graded by Dr. C.)

Continue projects - smaller scale
Week 6:
Feb 15 & 17

Continue projects - smaller scale

Each person's portion of project due

Oral presentations with peer review
(email comments to the presenter and cc Dr. C. Your comments will be part of your class participation grade.)

Week 7:
Feb 22 & 24

Conclude small scale project presentations

What blueberry projects shuold we do for the second half?

Tutorial #1 Assignments: due Feb. 24

First methodology tutorial Due (graded by Dr. C.)
Discuss and investigate whole-genome projects

null Week
Feb 28 - Mar 4

Spring Break

Spring Break

Week 8:
Mar 8 & 10

Continue blueberry projects

Blueberry Genome Database

Artemis Visualization Tool (.jar file)

PDF tutorial on Artemis (fish example)

Pymol script for extracting scaffold of interest from 454 sequences.


Continue blueberry projects

Week 9:
Mar 15 & 17
Continue blueberry projects

Continue blueberry projects
Week 10:
Mar 22 & 24

Continue blueberry projects

Design experimental testing?

Continue research
Week 11:
Mar 29 & 31

Prelimonary Oral Presentations

Guest visitor: Dr. Phil Meneely from Haveford College

Continue research

Week 12:
Apr 5 & 7

Continue research

Assess Status and Agree on Endgame

Write the final paper

Week 13:
Apr 12 & 14

Oral Presentation #2 on your second blueberry project
peer feedback - graded by Dr. C.

Finish final paper
Week 14:
Apr 19 & 21

No Class - write draft

First draft of final paper due
Bring Hard Copy to collect comments form peers
Peer review of draft paper (comments graded by Dr. C.)
Week 15:
Apr 26 & 28
May 3
Easter Break

No final exam

Final final paper due (as Word file) submitted by noon on May 3

Course Evaluations

Grades will be based on: glossary entries (10% total grade); two online tutorials for annotation process (20% total); peer review of tutorial (10% total grade); intermediate scale project and final research paper (focus TBD; 25% total grade); two oral presentations (30% total grade) and class participation (5% total grade). The exact nature of the papers cannot be determined at this point. You will use the course wiki page as an online lab notebook to track your daily progress. Keep in mind that your work will be the foundation that investigators will use for subsequent research.

Grading Scale:

Conversion of Percentages to Letter Grades
A = 100 - 95 A- = 94 - 92
B+ = 91 - 89 B = 88 - 86 B- = 85 - 83
C+ = 82 - 80 C = 79 - 77 C - = 76 - 74
D+ = 73 - 71 D = 70 - 68
F = < 67

Genomics Concentration

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