Dot Plots
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![Page 1: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/1.jpg)
Dot Plots
![Page 2: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/2.jpg)
DNA dot plots
Identification of regions of – Similarity between two sequences– Insertions-deletions: Introns– Repetitive regions (self-self analysis)– Inverted repeats
![Page 3: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/3.jpg)
Repeats
• All DNA sequences contain repeats
![Page 4: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/4.jpg)
Repeats
• All DNA sequences contain repeats
![Page 5: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/5.jpg)
Window size
• Window size 1
![Page 6: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/6.jpg)
Window size
• Window size 9
![Page 7: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/7.jpg)
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
![Page 8: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/8.jpg)
Exercise
CCTAAAGG
G
G
A
A
A
T
C
C
Sequence 1
Seq
uenc
e 2
Window size 1
Identity
![Page 9: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/9.jpg)
Exercise
CCTAAAGG
G
G
A
A
A
T
C
C
Sequence 1
Seq
uenc
e 2
Window size 3
Not considered
![Page 10: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/10.jpg)
Exercise
CCTAAAGG
G
3G
A
A
A
T
C
C
Sequence 1
Seq
uenc
e 2
Window size 3
GGAGGA
= 3 / 3 identities
![Page 11: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/11.jpg)
Exercise
CCTAAAGG
G
3G
2A
A
A
T
C
C
Sequence 1
Seq
uenc
e 2
Window size 3
GGAGAA
= 2 / 3 identities
![Page 12: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/12.jpg)
Exercise
CCTAAAGG
G
3G
2A
1A
A
T
C
C
Sequence 1
Seq
uenc
e 2
Window size 3
GGAAAA
= 1 / 3 identities
![Page 13: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/13.jpg)
Exercise
CCTAAAGG
G
3G
2A
1A
0A
T
C
C
Sequence 1
Seq
uenc
e 2
Window size 3
GGAAAT
= 0 / 3 identities
![Page 14: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/14.jpg)
Exercise
CCTAAAGG
G
000123G
001232A
012321A
013210A
131100T
310000C
C
Sequence 1
Seq
uenc
e 2
Window size 3
![Page 15: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/15.jpg)
Introns
mRNA
Gen
e
Introns are spliced out in the mRNA
}
}}
}
![Page 16: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/16.jpg)
Protein dot plots
![Page 17: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/17.jpg)
CLC Combined Workbench
![Page 18: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/18.jpg)
Ankyrin repeat protein
![Page 19: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/19.jpg)
HIV Long Terminal Repeats
![Page 20: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/20.jpg)
Di-nucleotide repeats
![Page 21: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/21.jpg)
Repetitive regions
![Page 22: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/22.jpg)
Exercise: Inverted repeats
![Page 23: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/23.jpg)
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
![Page 24: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/24.jpg)
Genome dot plots: inverted repeatsAnalysis of a random sequence of Homo sapiens chromosome 7 reveals numerous short inverted repeats
![Page 25: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/25.jpg)
The human Alu sequence
A self-self plot reveals some repetitive regions.
![Page 26: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/26.jpg)
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
![Page 27: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/27.jpg)
WD-repeat proteinsIdentity matrix Blosum45 matrix
![Page 28: Dot Plots](https://reader035.fdocuments.net/reader035/viewer/2022081519/56813524550346895d9c8a7d/html5/thumbnails/28.jpg)
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