Dotplots for Bioinformatics
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Transcript of Dotplots for Bioinformatics
Dot plots
Dr Avril [email protected]
Note: this talk contains animations which can only be seen by downloading and using ‘View Slide show’ in Powerpoint
Dot plots
• How can we compare the human & Drosophila melanogaster Eyeless protein sequences?One method is a dotplot
• A dotplot is a graphical method for assessing similarityMake a matrix (table) with one row for each letter in sequence 1, & one column for each letter in sequence 2Colour in each cell with an identical letter in the 2 sequencesRegions of local similarity between the 2 sequences appear as diagonal lines of coloured cells (‘dots’)
eg. for sequences ‘RQQEPVRSTC’ and ‘QQESGPVRST’:
Regions of local similarity between the 2 sequences appear as diagonal lines Some off-diagonal dots may be due to chance similarities
Sequence 2
Sequence 1
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Problem• Make a dot-plot for DNA sequences “GCATCGGC” &
“CCATCGCCATCG”. Are there regions of similarity?
Answer• Make a dot-plot for DNA sequences “GCATCGGC” &
“CCATCGCCATCG”. Are there regions of similarity?
CATCG in sequence 1 appears twice in sequence 2
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• If you colour in all cells with an identical letter, some dots may be due to chance similarities
• Therefore, it is common to use a threshold to decide whether to plot a ‘dot’ in a cellA window of a certain size (eg. window size = 3) is moved up all possible
diagonals, one-by-oneA score is calculated for each position of the window on a diagonal : the number of identical letters in the windowIf the score is equal to or above the threshold (eg. threshold = score of
2), all the cells in the window are coloured inThe choice of values for the window size and threshold for the dot plot
are chosen by trial-and-error
Dot plots with thresholds
Score = 1, < thresholdScore = 0, < thresholdScore = 0, < thresholdScore = 1, < thresholdScore = 2, ≥ thresholdScore = 2, ≥ threshold → colour inScore = 2, ≥ threshold → colour inScore = 2, ≥ threshold → colour inScore = 2, ≥ thresholdScore = 3, ≥ threshold → colour inScore = 3, ≥ threshold
eg. for sequences “GCATCGGC” and “CCATCGCCATCG” , using a window size of 3, and a threshold of ≥2:
and so on....
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Score = 0, < threshold
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Score = 0, < threshold
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Score = 1, < threshold
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Score = 1, < threshold
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Score = 1, < threshold
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Score = 1, < threshold
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Score = 0, < threshold
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Score = 0, < threshold
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Score = 0, < threshold
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Score = 0, < threshold
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Score = 2, ≥ threshold
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= the sliding window
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• A dot plot of fruitfly & human Eyeless proteins:
Do you think we chose a good value for the window-size and threshold?
Real data: fruitfly & human Eyeless
Human Eyeless
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Window-size = 10,Threshold = 3
Real data: fruitfly & human Eyeless• Here is a dot plot of fruitfly and human Eyeless proteins, made
using windowsize=10, threshold=5:
Are there any regions of similarity?
Human Eyeless
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Window-size = 10,Threshold = 5
• AdvantagesA dot plot can be used to identify long regions of strong similarity between two sequences It produces a plot, which is easy to make and to interpretIt can be used to compare very short or long sequences (even whole chromosomes – millions of bases)
• DisadvantagesIt is necessary to find the best window size and threshold by trial-and-errorA dot plot can only be used to compare 2 sequences, not >2 sequencesIt doesn’t tell you what mutations occurred in the region of similarity (if there is one) since the two sequences shared a common ancestor
Pros and cons of dot plots
• dotPlot() function in the SeqinR R libraryAllows you to specify a windowsize and threshold
If the score in a window is ≥ than the threshold, colours in the 1st cell in the window (not all cells)
• EMBOSS dottupAllows you to specify a windowsize but not a thresholdIf all cells in a window are identities, it colours in all cells in the window
• EMBOSS dotmatcherAllows you to specify a windowsize and thresholdInstead of using the number of identities in a window as the window score, it calculates a more complex score based on the similarities of the bases/amino acids
Software for making dotplots
Problem• Make a dot-plot for amino acid sequences
“RQQEPVRSTC” and “QQESGPVRST”, using a window size of 3, and a threshold of ≥3
Answer• Make a dot-plot for sequences “RQQEPVRSTC” and “QQESGPVRST”,
using window size: 3, threshold: ≥3
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Further reading• Chapter 3 in Introduction to Computational Genomics Cristianini & Hahn• Practical on dotplots in R in the Little Book of R for Bioinformatics:
https://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/src/chapter4.html