Dot matrix seminar

INTRODUCTION
• In computional biology a dot plot is a graphical methods
for comparing two biological sequences and identifying
region of close similarity
• It is type of recurrence plot (graph of horizontal and
vertical axis

HISTORY
• These are introduced by Gibbs and Mclntyre in 1970
• These plot are two dimensional matrices that have
sequences of the proteins being compared along the vertical
and horizontal axis.
• Individual cells in matrix can be shaded black,if the residue
are identical
• Thus matched sequences run of diagonal lines across the
matrix.

PRINCIPLE
• The principle used to generate the dot plot is:
• The top X and the left y axes of a rectangular array are used to represent the two
sequences to be compared
• Calculation:
• Matrix Columns = residues of sequence 1
Rows = residues of sequence 2

EXAMPLE
• Seq 1: TWILIGHTZONE
• Seq 2: MIDNIGHTZONE Matrix= 12 * 12
• A dot is plotted at every co-ordinate where there is similarity between the bases

DOT PLOT INTERPRETATION
• Seq1: ATGATAT
• Seq2: ATGATAT

SIMPLE PLOT TERMS
• Window: size of sequence block used for comparison.
example:
window = 1
• Stringency = Number of matches required to score
positive.
example:
stringency = 1 (required exact match)

DOTPLOT SCORING
• Dotplot- matrix, with one sequence across top, other down side. Put a dot, or 1, where ever
there is identity.
G A T C T
G
A
T
C
T

DOTPLOT SCORING
there is identity.
G A T C T
G
A
T
C
T
.

DOTPLOT SCORING
there is identity.
G A T C T
G
A
T
C
T
... .

DOTPLOT SCORING
there is identity.
G A T C T
G
A
T
C
T
... ... .

G A T A C T G C G A T A C T G C G C A
G 1 1 1 1 1
A 1 1 1 1 1
T 1 1 1 1 1
A 1 1 1 1
C 1 1 1 1 1
T 1 1 1 1
G 1 1 1 1
C 1 1 1 1
G 1 1 1
A 1 1 1
T 1 1
A 1
C 1 1 1
T 1
G 1 1
C 1 1
G 1
C 1
A 1

G A T A C T G C A T C G T C A C T C A
G 1 1 1
A 1 1 1 1 1
T 1 1 1 1 1
A 1 1 1 1
C 1 1 1 1 1 1
T 1 1 1 1
G 1 1
C 1 1 1 1 1
A 1 1 1
T 1 1 1
C 1 1 1 1
G 1
T 1 1
C 1 1 1
A 1 1
C 1 1
T 1
C 1
A 1

INTRAGENIC COMPARISON
• Rat Groucho Gene

INTERGENIC COMPARISON
• Rat and Drosophila Groucho Gene

• Nucleotide sequence contains three
domains.

domains.
• 50 - 350 - Strong conservation
• Indel places comparison out of register

domains.
• 450 - 1300 - Slightly weaker conservation

ANALYSIS OF DOT PLOT MATRIX
• Principal diagonal shows identical sequence.
• Global and local alignment are shown.
• Multiple diagonal indicate repeatation
• Reverse diagonal (perpendicular to diagonal) indicate
INVERSION.
• Reverse diagonal crossing diagonal (X) indicate
PALINDROMES.
• Formation of box indicate the low complexity region

PALINDROMIC SEQUENCE
• A palindromic sequence is a nucleic acid sequence (DNA or RNA) tha is same
whether read 5' to 3' on one strand or 5' to 3' on the complementary strand with
which it forms a double helix.

INVERTED REPEAT
• An inverted repeat is sequence of nucleotides followed downstream by its
reverse complement.
• Inverted repeat: abcdeedcbafghijklmno

LOW-COMPLEXITY REGIONS
• Low-complexity regions in sequences can be found as regions around the
diagonal all obtaining a high score. Low complexity regions are calculated from
the redundancy of amino acids within a limited region.

DOT PLOT SOFTWARE
• we can use the EMBOSS package, which are following:
 Dotmatcher
 Dotpath
 Polydot
 Dottup
(http://emboss.bioinformatics.nl/cgi-
bin/emboss/dottup

APPLICATION
• Shows the all possible alignment between two nucleic
acid and amino acid sequences.
• Help to recognise large region of simiarity.
• An excellent approach for finding sequence transposition.
• To find the location of genes between two genomes.
• To find the non sequential alignment.

LIMITATION
• For longer sequence, memory required for the graphical
representation is very high. So long sequence can not be aligned.
(only 2 sequence can align at a time)
• Lots of insignifcant matches makes it noisy (so many off diagonal
appear).
• Time required to compare two sequences is proportional to the
product of length of the sequences time of the search window. (not
very quick)
i.e, higher efficiency of short sequence.
Low efficiency of long sequence.

GAP PENALITY
• Gap penality is a method of scoring alignment of two or more sequence.
• when a gap is inserted in an sequence it matches more than the sequence
without gap insertion.
• Too many gap can cause an alignment to become meaningless.
Types of gap penality
Constant
Linear
affine

TYPES OF GAP PENALITY
Constant
This is the simplest type of gap penality and a fixed negative score is given to
every gap, regardless of its length.
ATTGACCTGA EACH MATCH=1 SCORE 7-1=6
AT CCTGA WHOLE GAP=1

Linear
The linear gap penalty takes into account the length (L) of each insertion/deletion
in the gap.
ATTGACCTGA EACH MATCH =1
AT CCTGA EACH GAP = -1
The score here is (7 − 3 = 4).

Affine
 Most widely used gap penality and it combines both linear and
constant gap penality.
 Penality is based on form of A+B.L
 A is known as the gap opening penalty, B the gap extension penalty
and L the length of the gap.
 Gap opening refers to the cost required to open a gap of any length,
and gap extension the cost to extend the length of an existing gap
by 1.

REFERENCES
• Bioinformatics concepts, skill & applications, second edition by
S.C.Rastogi, Namita Mendriatta, Parag Rastogi
• http://en.wikipedia.org/wiki/Dot_plot_%28bioinformatics%29
• http://lectures.molgen.mpg.de/Pairwise/DotPlots/
• https://ugene.unipro.ru/wiki/pages/viewpage.action?pageId=4
227426
• http://www.clcsupport.com/clcgenomicsworkbench/650/Examples
_interpretations_dot_plots.html

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