Part 1: Smith-Waterman Algorithm

Instructions:

1. Copy the "STS protein query sequence" from the week 3 links page (This is the one

letter code for the protein encoded by the Resveratrol synthase gene, the gene that

catalyzes the final step in the resveratrol synthesis pathway). Be sure to include the

">STS query" on the first line, or the program won't accept it.

2.

Go to https://www.ebi.ac.uk/Tools/sss/ and choose SSEARCH, then "protein". This will

do a Smith-Waterman local alignment on your protein sequence.

3. Choose the UniProtKB/TrEMBL database (under Step 1 on the page)

4. Paste the STS protein query sequence into the paste window

5. Choose SSEARCH under step 3, then click "More options". Here you will find a number

of parameters including the substitution matrix. Search UniProt using three different

substitution matrices:

• BLOSUM 50

• PAM 120

• PAM 250

Be patient, the calculation will take a while.

Questions:

1. What is the name and score of the best hit for each matrix?

2. What is the e-value of the best hit for each matrix?

3. Why do you think the results may have changed?

4. What do e-values mean and how do we interpret them?