Tutorial 7

1) Calculating Pairwise Alignment Scores





Alignment 1:



A G T G C A
A T A G A -




Alignment 2:



A G T G C A
A - T A G A




Alignment 3:



A G T - G C A
A - T A G - A


Question 1a: Calculate the scores of the above DNA alignments if the score of a match is 2, a mismatch is -1 and a gap is -3. Which alignment is the best?

Alignment 1:

Alignment 2:

Alignment 3:

Which alignment is the best?


Question 1b: Do the same again when the score of a match is 3, a mismatch is -1 and a gap is -2. Which alignment is the best now?

Alignment 1:

Alignment 2:

Alignment 3:

Which alignment is the best now?





2) BLOSUM Matrix





Alignment 1:



- lys arg gly ser
arg lys ala gly -




Alignment 2:



lys arg gly ser
arg lys ala gly


The BLOSUM matrices are substitution matrices used for sequence alignment of proteins. The BLOSUM62 matrix is here.

Question 2: Calculate the alignment score for the two protein alignments above using the BLOSUM62 matrix and a gap penalty of -3.

What is the BLOSUM62 score for residue pairs [Asp, Gln] and [Asn, Leu]? Which pair is more similar?

Following the link above, when would you want to use BLOSUM62 instead of BLOSUM80?

Alignment 1:

Alignment 2:

Which alignment is better?





3) Extracting optimal alignment from table



- A C C G T
- 0 -3 -6 -9 -12 -15
A -3 2 -1 -4 -7 -10
C -6 -1 4 1 -2 -5
G -9 -4 1 3 3 0
C -12 -7 -2 3 2 2















The above table was generated by the Needleman & Wunsch Algorithm and represents alignments of the sequences: ACCGT / AGCG, and with a match score of +2, a mismatch score of -1 and a gap score of -3.

Question 3: Extract the optimal alignments from this table.

What is the score of an optimal alignment?

Optimal alignment 1:

Optimal alignment 2:



4) Extracting optimal local alignment from table



- G T A T G
- 0 0 0 0 0 0
T 0 0 2 0 2 0
A 0 0 0 4 1 1
T 0 0 2 1 6 3
A 0 0 0 4 3 5















The above table was generated by the Smith & Waterman Algorithm and represents alignments of the sequences: GTATG / TATA, and with a match score of +2, a mismatch score of -1 and a gap score of -3.

Question 4: Extract the optimal alignment(s) from this table.

What is the score of an optimal alignment?

Optimal local alignment(s):





5) Needleman & Wunsch Algorithm

Seq1: A   C   G   G   T   A


Seq2: C   G   A   T   A


Question 5: Using the Needleman/Wunsch algorithm, with a match score of +2, a mismatch score of -1 and a gap score of -3, fill out the table below and find the optimal alignment(s) of sequences 1 and 2.

- A C G G T A
-
C
G
A
T
A


What is the optimal alignment(s)?


What is the score of an optimal alignment?



6) Bonus question: linear and affine gap penalties





Alignment 1:



- - A T - G G C
G T A T G G G C




Alignment 2:



A T - - - G G C
G T A T G G G C

Question 6a: Linear penalty: calculate the scores of the above DNA alignments if the score of a match is 2, a mismatch is -1 and a gap is -3.

Alignment 1:

Alignment 2:

Question 6b: Affine penalty: calculate the scores of the above DNA alignments if the score of a match is 2, a mismatch is -1, the gap opening penalty is -5 and the gap extension penalty is -1.

Alignment 1:

Alignment 2: