Alignment:

1
Alignment Global, local, repeated and
overlaping Jan 21 2004
2

1. Global Alignment by the Needleman-Wunsch
   algorithm

From scoring matrix S
Linear gap penalty
F

0
-d
-nd
-2d
-d
F(2,1)
F(,1)
F(1,1)
F(n,1)
-2d
F(1,2)
F(n,2)
F(2,2)
F(,2)

Total score
F(1,)
F(2,)
F(,)
F(n,)
F(1,m)
-md
F(2,m)
F(n,m)
F(,m)
Trace back
3
2. Local alignment by the Smith-Waterman algorithm
To break uniformative pairwise combinations
F

0
0
0
0
Total score
0
F(2,1)
F(,1)
F(1,1)
F(n,1)
0
0
F(1,2)
F(n,2)
F(2,2)
F(,2)

F(1,)
F(2,)
max
F(,)
F(n,)
F(1,m)
0
F(2,m)
F(n,m)
F(,m)
Trace back
4
3. Repeated matches

• could be used to search for a repeated domain or
  motif in a protein
• care is required in implementation of this
  algorithm as it is asymmetric in the sense that
• x represents the sequence containing the domain
• y represents the sequence in which we look for
  repeated matches

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3. Repeated matches

• Traceback from M(n1,0) records the best
  alignment
• The global alignment contains matched and
  unmatched regions
• Only matches above a threshold, T, are recorded
• Scores are computed relative to this threshold
• Changing T will thus affect the outcome of the
  algorithm
• If T is too large, some matches will be missed
• If T is too small, match regions may be split and
  too many weak matches may be found
• Variation of this algorithm
• WATERMAN-EGGERT ALGORITHM (1987)

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threshold value
3. Repeated matches
(Local alignment)
Total score
F
F(2,0)
F(,0)
0
F(1,0)
F(n,0)
F(n1,0)
Trace back
7
4. Overlap matches

• global alignment strategy which does not penalize
  overlapping ends
• Algorithm is as per global alignment, except at
  initialization and a slight alteration of
  traceback
• Traceback
• starts from the maximum recorded element in the
  mth row and the nth column
• i.e., maxF(n,0), F(n,1),.,F(n,m), F(n-1,m),
  F(n-2,m),, F(0,m)
• ends when the 0th row or column is reached.
• Hitting the 0th row corresponds to the end of
  sequence x
• Hitting the 0th column corresponds to the end of
  sequence y

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threshold value
4. Overlap matches
------
(Local alignment)
(Global alignment)
F
F(2,0)
F(,0)
0
F(1,0)
F(n,0)
F(0,m1)
Total score
0
max
Trace back