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

• Window size 1

Window size

• Window size 9

Exercise

CCTAAAGG

G

G

A

A

A

T

C

C

Sequence 1

Seq

uenc

e 2

Practice for,a) window size 1b) window size 3

Exercise

CCTAAAGG

G

G

A

A

A

T

C

C

Sequence 1

Seq

uenc

e 2

Window size 1

Identity

Exercise

CCTAAAGG

G

G

A

A

A

T

C

C

Sequence 1

Seq

uenc

e 2

Window size 3

Not considered

Exercise

CCTAAAGG

G

3G

A

A

A

T

C

C

Sequence 1

Seq

uenc

e 2

Window size 3

GGAGGA

= 3 / 3 identities

Exercise

CCTAAAGG

G

3G

2A

A

A

T

C

C

Sequence 1

Seq

uenc

e 2

Window size 3

GGAGAA

= 2 / 3 identities

Exercise

CCTAAAGG

G

3G

2A

1A

A

T

C

C

Sequence 1

Seq

uenc

e 2

Window size 3

GGAAAA

= 1 / 3 identities

Exercise

CCTAAAGG

G

3G

2A

1A

0A

T

C

C

Sequence 1

Seq

uenc

e 2

Window size 3

GGAAAT

= 0 / 3 identities

Exercise

CCTAAAGG

G

000123G

001232A

012321A

013210A

131100T

310000C

C

Sequence 1

Seq

uenc

e 2

Window size 3

Introns

mRNA

Gen

e

Introns are spliced out in the mRNA

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}}

}

Protein dot plots

CLC Combined Workbench

Ankyrin repeat protein

HIV Long Terminal Repeats

Di-nucleotide repeats

Repetitive regions

Exercise: Inverted repeats

Exercise: Inverted repeats

CCTAAAGG

G

G

A

T

T

T

C

C

Sequence 1

Rev

erse

com

plem

ent Make a dot plot with the sequence

against the reverse-complement of the sequence. Now diagonals represent inverted repeats.

Window size 3

Genome dot plots: inverted repeatsAnalysis of a random sequence of Homo sapiens chromosome 7 reveals numerous short inverted repeats

The human Alu sequence

A self-self plot reveals some repetitive regions.

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 proteinsIdentity matrix Blosum45 matrix

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