Transcript Gene regulatory networks - DIT School of Computing

Assessment of sequence
alignment
Lecture 10
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Introduction
• The Dot plot Matrix visualisation matching
tool:
– Basics of Dot plot
– Examples of Dot plot matching sequences
– Tandems repeats self matching
– Inverted repeats: genetic palindromes
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Sequence alignment Analysis
• In order to measure the degree of similarity
between sequences they must first be aligned
to maximise the matching score (refer to
lecture 11):
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Example 1
I am from Cork
I am not from Cork
****
(4 matches out of 18; based on
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Example 2
I am ---- from Cork
I am not from Cork
**** **********
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(14 matches out of 18; based on length
of bottom string)
length of bottom string)
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The Dot plot
• A “better” way of doing this is to represent each
sequence as a table or matrix, where one
sequence represents the rows and the other the
columns. The Dot plot Matrix is a visual way of
seeing the alignment between two sequences:
– The first sequence (query sequence) represents the
rows and the other sequence (subject sequence)
represents the columns.
– All elements (row/column) are checked for a match
and if there the cell is marked.
– This will show all areas of both sequences where
matches occur.
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Dot plot
• Consider the following:
– Diagonal lines represent a alignments
(match)
– Horizontal lines between aligned
sequences indicate gaps are required
(where the gaps indicate a
deletion/insertion)
–
• This has four “potential” aligned
sequences:
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–
–
–
D->Y;
H->N
R->0
0->H
• Longest sequence of alignments are:
– “THIS” ; and “SEQUENCE“;
– “IS” would be considered as gaps
adapted from understanding
bioinformatics p. 77
• The pink dots: they can represent
noise (spurious alignments)
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Dot plot Matrix: purpose
• This allows us to visualise areas of “local
alignment” as opposed to global alignment.
• One of the main purpose to find domains /
motifs that match . This could be useful for
many reasons; e.g. promoter factor binding
site, finding exons….
• For visualisation of pair-wise alignment you
have one query on the x-axis and the other on
the y-axis.
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Dot Plot noise
This shows the effect of noise (blue line has be been inserted to highlight alignment if
interest. The figure on the left represents SH2 sequence (sample files ) plotted against
inself. The one on the right has been filter; in this case an alignment must be at least 10
residues long with a score of 3. adapted from understanding bioinformatics p. 77
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Dot plot Matrix: imperfect match
• Some alignments require
gaps to increase the
matching score; the gaps
are used represent
inclusion/deletion
mutations
• The diagram shows that
most of the 2 sequences
are aligned. Where there
are gaps indicates areas
of non-alignment or
mismatches: gaps or
substitutions
Adapted from: dotplot example
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Refer to saved web page
Dot plot: example 1
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Dot plot: example 1
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Dot plot for Tandem Repeats
• The human genome has many tandem repeats
small sequences of nucleic acids (bases)/ Amino
acids that are repeated and are ubiquitous in
genomes and can compromise 50% of genome.
(Richard 2008)
• They can be used as genealogical markers
• To determine specific regions of interest; e.g.
introns
• Play a significant part in evolution Gemayel 2010
• An example of a protein with multiple repeats is
human mucin (Baxevanis 2005 p. 297)
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Dot plot of tandem repeats
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Tandem repeat as a sequence
Tandem repeat 1
A
B
R
A
C
A
D
A
B
R
A
C
A
D
A
B
R
A
A
B
R
A
C
A
D
A
B
R
A
C
A
D
A
B
R
A
Tandem repeat 2
A
B
R
A
C
A
D
A
B
R
A
C
A
D
A
B
R
A
A
B
R
A
C
A
D
A
B
R
A
C
A
D
A
B
R
A
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Tandem repeat dot plot
• To determine if there is tandem repeats the
sequence is compared with itself (refer table 1)
• The more diagonals the more repeats
• The diagonals at the bottom left compare the
start with the finish
• The fact the main diagonal means the both
sequences are the same .
• The lines are symmetrical around the main
diagonal:
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Tandem repeats (Example)
•
BRCA2 gene has a number of BRC repeats (39 residues long. The diagram shows
two plots: one with noise (unfiltered) and the other showing two repeating
sequences. Adapted from Figure 4.3 understanding bioinformatics
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Genetic “Palindromes”
•
A palindrome is a word that is spelt the same from right to left as well as from left
to write: This will give an “X” shaped dot-plot. (try; eye, navan; never odd or even
…..)
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Remember left to right is (5’ to 3’) on primary strand and right to left is (5’ to 3’)
on the complimentary strand. Alternatively it means a match between a strand and
its reverse compliment.
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2 possible types of “Genetic Palindromes” [the difference being that the left to
right, read, is on one strand while the right to left, read, is on its complimentary
strand]:
– Restrictive enzymes such as EcoR1:
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5’ GAATTC 3’
3’ CTTAAG 5’
– Inverted repeats
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On different segments; each repeat read the same (GTGAG) but in opposite directions. An example is
promoter region for the CAP protein in the lac operon :
–
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5‘ GTGAGnnnCTCAC 3'
3' CACTCnnnGAGTG 5’
What will the dot plot for the above 2 sequences look like.
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Supplementary reading
• The following provides links to further reading
on DOT PLOTS.
– introduction to dotplot (figure 6 gives a more
indepth view of different types of plots referred to
above: alignment, alignment with gaps, tandem
repeats, palindromes…..
– Inverted repeats and dotplot. (more advanced
analysis of plots for inverted repeats)
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Exam Question
• Describe, using a suitable example, how to
construct a dot plot matrix for the alignment
of DNA/AA sequences. (10 marks)
• Describe the significance of two types of
repeating sequences found in DNA sequences
(6 marks)
• Explain, using suitable examples, how the DOT
plot matrix can find the two types of repeating
regions [what is plotted against what and
what will the DOT PLOT look like] (14 marks)
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References
• Baxevanis A.D. 2005 Bioinformatics: a practical guide to the
analysis of genes and proteins chapter 11; Wiley
• Klug, W. S. (2010); the essentials of genetics; 7th ed Pearson
Education
• Gemayel, R. et al 2010 Variable tandem repeats accelerate
evolution of coding and regulatory sequences. Annu Rev
genet 44: 445-477
• Richard, G.F. (2008) Comparative genomics and molecular
dynamics of DNA repeats in eukaryotes. Microbiol Mol biol
rev 2008 Dec;72(4):686-727
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