Discuss the Tillier Collins paper
- Strand bias (slides here)
- example of simple perl scripts:
- (perl script to extract top scoring hits is here (pdf))
- (perl script to replace gi number with position on the genome is here (pdf) (faa_sample, feature_table sample)
- (perl script to make gnuplot is here (pdf), output for Thermotoga maritima vs Th. petrophila is here, Gene plots for comparison between different Aeromonas species are here, here and here). Discuss: Which recombination events could have created these patterns?
If time:
