alignment methods
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Alignment methodsOctober 16, 2012Return Quiz 1 todayReturn homework on Thursday.Homework from last week due on ThursdayLearning objectives- Needleman Wunsch Global Alignment program.New Homework exercises #5 and #6 from Chapter 5.
Three steps
Initialization
Matrix fill
Traceback
Alignment A Sequence 1: ADCDN-R-CKCRWP Sequence 2: AWC-NDRQCLCR-P Score: 10101010101101Total Score: 8Alignment B Sequence 1: ADC-DNR-CKCRWP Sequence 2: AWCND-RQCLCR-P Score: 10101010101101Total Score: 8
A W C N D R Q C L C R P
A 1
D 1
C 1 1 1
D 1
N 1
R 1 1
C 1 1 1
K
C 1 1 1
R 1 1
W 1
P 1
Matrix fill
Traceback
W(L) = gL equation 5.1where g is the cost of a single gap.
Affine gap penaltyW(L) = gopen + gext(L) equation 5.2
Total score = equation 5.3
Modified N-W Global alignment with linear gap penalty
Sequence 1: ADCDN (vertical sequence)Sequence 2: AWCN (horizontal sequence)
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