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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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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

C

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A

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C

Exercise

Practice for,

a) window size 1

b) window size 3

Sequence 2

Sequence 1


Exercise1

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G

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C

Exercise

Window size 1

Identity

Sequence 2

Sequence 1


Exercise2

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C

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Exercise

Window size 3

Not considered

Sequence 2

Sequence 1


Exercise3

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3

G

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C

Exercise

Window size 3

GGA

GGA

Sequence 2

= 3 / 3 identities

Sequence 1


Exercise4

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2

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3

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Exercise

Window size 3

GGA

GAA

Sequence 2

= 2 / 3 identities

Sequence 1


Exercise5

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C

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A

1

A

2

G

3

G

G

G

A

A

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C

Exercise

Window size 3

GGA

AAA

Sequence 2

= 1 / 3 identities

Sequence 1


Exercise6

C

C

T

A

0

A

1

A

2

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3

G

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A

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C

Exercise

Window size 3

GGA

AAT

Sequence 2

= 0 / 3 identities

Sequence 1


Exercise7

C

C

0

0

0

0

1

3

T

0

0

1

1

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1

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1

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1

0

A

1

2

3

2

1

0

A

2

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1

0

0

G

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2

1

0

0

0

G

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C

C

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