Sequence Alignment I Dot Matrices

1
Sequence Alignment IDot Matrices
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Reading

• Mount, Chapters 1, 2, and 3 (up to page 94)

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Why compare sequences?

• To find whether two (or more) genes or proteins
  are evolutionarily related to each other
• To find structurally or functionally similar
  regions within proteins

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Similar genes arise by gene duplication

• Copy of a gene inserted next to the original
• Two copies mutate independently
• Each can take on separate functions
• All or part can be transferred from one part of
  genome to another

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Sequence Comparison Methods

• Dot matrix analysis
• Dynamic Programming
• Word or k-tuple methods (FASTA and BLAST)

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Dot matrices
c
g
g
a
c
a
c
a
c
g
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Dot matrix comparison
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Interpretation

• Regions of similarity appear as diagonal runs of
  dots
• Reverse diagonals (perpendicular to diagonal)
  indicate inversions
• Reverse diagonals crossing diagonals (Xs)
  indicate palindromes

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Interpretation

• Can link separate diagonals to form alignment
  with gaps
• Each a.a. or base can only be used once
• Can't double back
• A gap is introduced by each vertical or
  horizontal skip

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Filtering

• Dot matrices for long sequences can be noisy due
  to insignificant matches
• Solution use a window and a threshold
• compare character by character within a window
  (have to choose window size)
• require certain fraction of matches within
  window in order to display it with a dot

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Dot plot comparison using windows
Window size 11 Stringency 7
(Put a dot only if 7 out of next 11 positions are
identical.)
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Uses for dot matrices

• Aligning two proteins or two nucleic acid
  sequences
• Finding amino acid repeats within a protein by
  comparing a protein sequence to itself
• Repeats appear as a set of diagonal runs stacked
  vertically and/or horizontally

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Repeats
Human LDL receptor protein sequence (Genbank
P01130) W 1 S 1 (Mount, Fig. 3.6)
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Repeats
W 23 S 7 (Mount, Fig. 3.6)
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Using substitution matrices

• Dots can have weights
• Some matches are rewarded more than others,
  depending on likelihood
• Use PAM or BLOSUM matrix (more on these later)
• Put a dot only if a minimum total or average
  weight is achieved
• See Mount, Fig. 3.5