Scoring Sequence Alignments Calculating E E = m · n · pS Expected number = number of possibilities · unit probability 1/32 Example: Expected number of a match of H H H H T ? Unit probability = ½ · ½ · ½ · ½ · ½

Scoring Sequence Alignments Calculating E E = m · n · pS Expected number = number of possibilities · unit probability 5/32 5 1/32 Example: Expected number of a match of H H H H T ? Number of possibilities = H H H H T H H H T H H H T H H H T H H H T H H H H

Scoring Sequence Alignments Calculating E E = m · n · pS Expected number = number of possibilities · unit probability Unit probability of match = pS = (¼) number of matches Number of possibilities = m · n (match can begin anywhere in query) (match can begin anywhere in target)

Scoring Sequence Alignments Calculating E E = m · n · pS Expected number = number of possibilities · unit probability Unit probability of match = pS = (¼) number of matches e ln(¼) · number of matches e -λ · number of matches

Scoring Sequence Alignments Calculating E E = K · m · n · e –λS SQ5. Calculate E from parameters of real Blast search

Protein Alignments PAM scoring tables SQ7. Amongst protein pairs that are 99% similar to each other, what fraction of arginines in one protein correspond to lysines in the other (at the equivalent position)? What fraction of arginines in one correspond to leucines in the other

Protein Alignments PAM scoring tables SQ7. Amongst protein pairs that are 99% similar to each other, …what fraction of arginines in one protein correspond to lysines in the other?

Protein Alignments PAM scoring tables SQ8. What PAM table would be appropriate to search for proteins about 50% identical to a query sequence?

Protein Alignments Log odds scoring tables U M 6 2 SQ10. What sequences would be found by VLI using a T value of 13?

Scenario 2: Genome comparison & Parsing It's often useful to know the size of an array.  One way to do this… my @a = ("red", "green", "blue"); my $size = @a print $size, "\n";

BlastN: Web version Checklist X 1. Filter the query sequence to remove repetitive regions 2. Find all query-target matches √ a. Extract a word from the query, using a sliding window √ b. Find an exact match of the word in the target sequence If no match, return to Step a c. Extend match in both directions √ X d. Calculate a score for the final match X e. Save matches whose scores exceed threshold f. Repeat a - e √ X 3. Rank the matches by their scores ~ 4. Print out the top matches.