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Sequence Alignment I Dot Matrices. Reading. Mount, Chapters 1, 2, and 3 (up to page 94). 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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Presentation Transcript
reading
Reading
  • Mount, Chapters 1, 2, and 3 (up to page 94)
why compare sequences
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
similar genes arise by gene duplication
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
sequence comparison methods
Sequence Comparison Methods
  • Dot matrix analysis
  • Dynamic Programming
  • Word or k-tuple methods (FASTA and BLAST)
dot matrices
Dot matrices

c

g

g

a

c

a

c

a

c

g

interpretation
Interpretation
  • Regions of similarity appear as diagonal runs of dots
  • Reverse diagonals (perpendicular to diagonal) indicate inversions
  • Reverse diagonals crossing diagonals (Xs) indicate palindromes
interpretation9
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
filtering
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
dot plot comparison using windows
Dot plot comparison using windows

Window size = 11

Stringency = 7

(Put a dot only if 7 out of next 11 positions are identical.)

uses for dot matrices
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
repeats
Repeats

Human LDL receptor protein sequence (Genbank P01130)

W = 1

S = 1

(Mount, Fig. 3.6)

repeats14
Repeats

W = 23

S = 7

(Mount, Fig. 3.6)

using substitution matrices
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