In-class problems

In-class Problems Week 4

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.

We can align gene sequences to determine their similarity within a single organism, or between multiple organisms. Although the earlier warning about sequence similarity not being sufficient proof of homology, we can still use alignment as a starting point for an investigation. You may remember that a pair of sequentially similar genes can be:

• Homologs if they have a shared evolutionary history, either:

  • Paralogs if they are in the same organism and were the result of a duplication event

  • Orthologs if they are in different organisms as a result of speciation

• Analogs if they are in different organisms but have a separate evolutionary origin.

With this in mind, consider the following questions:

• Given the gene sequences of a single organism, how would we find potential paralogs?

• Given the gene sequences of two organisms, how would we find potential orthologs?

• What additional evidence could we use from our work to support the argument that the gene-pairs are paralogs or orthologs?

You can use the genomes from Unix 1 to explore these questions, found at /nfs/teaching/551-0132-00L/1_Unix/genomes.

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