In-class problems

In-class Problems Week 5

Remember that for the in-class problems, you can use different resources (command line manual/help pages, browser-based searches, AI-based problem solving) to find an answer. There is no right or wrong approach to finding an answer to a problem.

Some simple features encoded by DNA can be found without complex models. Using command line tools and Python, how might you:

• Search for exact matches to a restriction enzyme recognition site? For instance, find the recognition site for EcoR1 online and then search for sites in the bacterial genomes in /nfs/teaching/551-0132-00L/1_Unix/genomes.

• Search for primer binding sites, allowing for one base mismatch? For instance, find the sequences for the 27F and 1492R primers that amplify the 16S rRNA and look for binding sites in the bacterial genomes in /nfs/teaching/551-0132-00L/1_Unix/genomes.

Imagine you had identified a new prokaryote and were interested in classifying its metabolic capabilities. You can either use your assigned genome or the E. coli/Salmonella genome pretending this is a new organism. With the introduced databases and methods in mind, consider the following questions:

• Is your organism capable of breaking down glucose into pyruvate by glycolysis?

• Does your organism encode for the enzymes required for lactose fermentation?

Note: There will be no example solutions for in-class-problems. It is expected that students take notes during the lecture. If questions come up, students can use the Slack-channels to receive help.