Part III: FASTA Algorithm

Instructions:

1. Go to

https://www.ebi.ac.uk/Tools/sss/ and select FASTA, then protein.

2. Choose UniProtKB/TrEMBL as your database (step 1)

3. Paste in your STS protein query sequence (step 2)

4. Click More options... on step 3 and run your queries for the following choices of

parameters:

Scoring Matrix

BLOSUM 50

BLOSUM 80

BLOSUM 80

BLOSUM 80

Gap Open

-10

-10

0

-64

Gap Extend

-2

-2

0

-16/nQuestions:

1. Did these calculations take as long as the Smith-Waterman search? If so, why?

2. Were the results different from the Smith-Waterman search? Why do you think this

happens?

3. What is the effect of changing to a higher cutoff BLOSUM matrix (i.e. from 50 to 80) and

what does it mean?

4. What is the effect of changing the Gap Open and Gap Extend parameters? Why do you

think you observed what you did?