Charles Hu Homework 5

Part 1

1. predicting the three-dimensional structure of a protein sequence;
   • Structure prediction is based on favorable energy conformation by assessing the amino acid interactions. Accurate sequence alignment will allow for accurate amino acid sequence prediction, thus leading to a viable protein form.
2. introducing random mutations into a protein sequence for the purposes of a directed (in vitro) evolution experiment;
   • Having a good alignment allows you to change small portions of the sequence at a time. This isolates specific mutations for future references in directed evolutionary experiments.
3. determining whether a particular bacterial gene has been introduced to its host genome via a "horizontal transfer" event;
   • Variations in the alignment before and after the transfer event confirms that a transfer has occurred, and by studying the specific aligned sequence, you can deduce whether the same bacterial sequence had been inserted.
4. attempting to identify regulatory elements (such as riboswitches) in a genome sequence.
   • It allows you to identify the activation site for those regulatory elements by studying the effects of specific mutations in a specific location.

Part 2

1. See attachment for perl program