Introduction to Bioinformatics

1
Introduction to Bioinformatics

• Dot Plots

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Dot Plots

• One of the simplest and oldest methods for
  sequence alignment
• Visualization of regions of similarity
• Assign one sequence on the horizontal axis
• Assign the other on the vertical axis
• Place dots on the space of matches
• Diagonal lines means adjacent regions of identity

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Simple Example

• Construct a simple dot plot for GCTGAA GCGAA
• One sequence goes horizontally, the other
  vertically
• Mark boxes w/ matched horizontal and vertical
  symbols
• Look for diagonal(s)
• Alignment
• GCTGAA
• GCT-AA

G C T G A A
G
C
T
A
A
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Another Example

• Construct a simple dot plot forGCTAGTCAGATCTGACGC
  TAGATGGTCACATCTGCCGC
• A long stretch of nearly identical residues is
  revealed starting at the fifth nucleotide of each
  sequence (GTCA-ATCTG-CGC).

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Sliding Window and Cutoff

• Problem
• Plot becomes noisy when comparing large, similar
  sequences
• Solution
• Sliding window (size w)
• Cutoff (value v)
• Consider w nucleotides at a time
• When at least v matches in a window, place a dot
  on the space where the window starts

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Example

• Same example with w 4 and v 3
• Compare to the previous plot. You make the call!

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Worksheet

• w 4 and v 3

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What else can it do (and how)?

• Gaps
• Inverse subsequence
• Repeats
• Palindrome
• Genome rearrangement
• Exon identification
• RNA structure prediction
• Nice tool for conceptualizing sequence-related
  algorithms