Faction 1: Comparative Genomics Lab Exercises

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Gene Prediction Homework

Faction 1

Due Friday 4/21/17 by 11:59:59 pm

1. BRIG (25 points) Use the FASTA files for samples OB007-OB0011 from /data/projects/comparative

Use the following reference genome: /data/home/jrowell32/data/the_reference/GCF_001690035.1_ASM169003v1_genomic_concatenated.fasta

a. Briefly describe the output of BRIG. (5 points)

b. Download BRIG and run it on the 5 sample genomes. Paste the figure below. https://sourceforge.net/projects/brig/ (10 points)

c. Briefly describe the output. (10 points)

2. HGTector (25 points)

a. What is horizontal gene transfer and why are we interested in it for this “outbreak investigation”? (10 points)

b. Git clone the master branch of the HGTector repository and run it with the --help option. This will run HGTector on the test dataset. (5 points)

c. Describe the output. (10 points)

Please email the submission to faction1.g4@gmail.com.

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