Dot Plots
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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
• 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