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Dot Plots. DNA dot plots. Identification of regions of Similarity between two sequences Insertions-deletions: Introns Repetitive regions (self-self analysis) ‏ Inverted repeats. Repeats. All DNA sequences contain repeats. Repeats. All DNA sequences contain repeats. Window size.

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Presentation Transcript
dna dot plots
DNA dot plots

Identification of regions of

  • Similarity between two sequences
  • Insertions-deletions: Introns
  • Repetitive regions (self-self analysis)‏
  • Inverted repeats
repeats
Repeats
  • All DNA sequences contain repeats
repeats1
Repeats
  • All DNA sequences contain repeats
window size
Window size
  • Window size 1
window size1
Window size
  • Window size 9
exercise

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Exercise

Practice for,

a) window size 1

b) window size 3

Sequence 2

Sequence 1

exercise1

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Exercise

Window size 1

Identity

Sequence 2

Sequence 1

exercise2

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Exercise

Window size 3

Not considered

Sequence 2

Sequence 1

exercise3

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Exercise

Window size 3

GGA

GGA

Sequence 2

= 3 / 3 identities

Sequence 1

exercise4

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Exercise

Window size 3

GGA

GAA

Sequence 2

= 2 / 3 identities

Sequence 1

exercise5

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Exercise

Window size 3

GGA

AAA

Sequence 2

= 1 / 3 identities

Sequence 1

exercise6

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Exercise

Window size 3

GGA

AAT

Sequence 2

= 0 / 3 identities

Sequence 1

exercise7

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Exercise

Window size 3

Sequence 2

Sequence 1

introns
Introns

}

Gene

Introns are spliced out in the mRNA

}

}

}

mRNA

exercise inverted repeats1

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Exercise: Inverted repeats

Window size 3

Make a dot plot with the sequence against the reverse-complement of the sequence.

Now diagonals represent inverted repeats.

Reverse complement

Sequence 1

genome dot plots inverted repeats
Genome dot plots: inverted repeats

Analysis of a random sequence of Homo sapiens chromosome 7 reveals numerous short inverted repeats

the human alu sequence
The human Alu sequence

A self-self plot reveals some repetitive regions.

the human alu sequence1
The human Alu sequence

A plot of the Alu sequence against its reverse-complement reveals its inverted repeat (palindromic) nature, seen as the diagonal along the entire sequence length

wd repeat proteins
WD-repeat proteins

Blosum45 matrix

Identity matrix

conclusion
Conclusion
  • Dot plots provide an intuitive view of sequence comparisons.
  • The sliding window size is important.
  • For proteins, substitution matrices can be used.
  • Dot plots can reveal
    • Repeats
    • Insertion/Deletions (such as introns)‏
    • Inverted repeats
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