1. Affine Gap Alignment
Marcus Bamberger

2. The Goal Write a global-align function Build off of the 6.1 lab
Incorporate Affine gaps

3. Alignment Graph as 3 Levels
How can we emulate this path in the 3-level graph? ε
loweri-1,j - ε middlei-1,j - σ σ
loweri,j = max { σ
upperi,j-1 - ε middlei,j-1 - σ
upperi,j = max {
loweri,j
middlei-1,j-1 + score(vi,wj)
upperi,j
middlei,j = max { ε

4. Data used Toy sequences UCSC genome – human chromosome 1
Repeated motif, interspersed with junk
GCATGCATGCAT and ACACACGCATACACACGCATACACACGCATACACAC
UCSC genome – human chromosome 1
IntronExonIntronExonIntron
ExonExonExon

5. gapAlign procedure
Inputs: string1, string2, gapStart, gapContinue, match, misMatch.
String1 >= string2
Backtrack tables and scoring tables all constructed simultaneously
Diagonal route, upper right to lower left
Alignment constructed according to scoring results, following backtrack table
Alignment printed, score given

6. Results gapContinue <= -0.1, all other scores 1/-1
“Clumping” occurs when gap creation/extension is overly penalized
Precise values depend on gap length necessary for motif matching
Setting gapContinue to 0 fixes these, assuming your string is constrained
Compared to my 6.1 alignment:
CTCGAGTCTAGAGCATTCGAGTCTAGAAGCATTCGAGTCTAGAAGCATTCGAGTCTAGAAGCATTCGAGTCTAGAA
GCAT GCAT GCAT GCAT
G C---A------T------G C---A------T------G C---A------T------G C--A T-----