to understand the concept of dot plot in bioinformatics

1. Dot-Plot
Presented By:
Ist
Year M.Sc Bioinformatics

2. Sequence Alignment
Significance of Sequence Alignment
Methods of Sequence Alignment
Dot Plot
Principle
Dot Plot Algorithm
Examples and interpretations of dot plots
Dot Plot Software
Application
Limitation
TABLE OF CONTENT:

3. Why Sequence Alignment ?
 Sequence Alignment is the procedure of comparing
Two (Pair-wise Alignment) or More (Multiple
sequence Alignment) sequences by searching for a
series of individual characters or character patterns that
are in the same order in the sequences.
 It is an Important First Step toward Structural and
Functional Analysis of newly Determined Sequence .
Sequence Alignment
Global
Alignment
Local
Alignment

4. PAIRWISE ALIGNMENT
01
GOLBAL ALIGNMENT
03
LOCAL ALIGNMENT
04
MULTIPLE SEQUENCE
ALIGNMENT
02
SEQUENCE
ALIGNMENT

5. In Global alignment, two sequences to be aligned over their
entire length.
Sequences that are quite similar and approximately Have
the same length are suitable for global alignment.
The alignment is performed from start to finish of the two
sequences in order to find the best possible alignment
GLOBALALIGNMENT :
Taking Entire Part of the Sequence

6. LOCALALIGNMENT :
 It only finds local regions with the highest level of
similarity between the two sequences and aligns
these regions without regard for the alignment of the
rest of the sequence regions.
Find the Best Matching subsequence

7. Significance of Sequence Alignment:
 Sequence alignment is useful for discovering Functional,
Structural, and Evolutionary information in biological
sequences
 Functional: DNA molecules that are very much alike or similar
in sequence analysis parlance probably have the same
regulatory role.- Protein molecules that are very much alike
probably have the same biochemical function
 Structural: Protein molecules that are very much alike
probably have the same 3-D structure
 Evolutionary: If two sequences from different organisms are
similar then there may have been a common ancestor
sequence, and the sequences are then defined as being
homologous .The alignment indicates the changes that could
have occurred between the two homologous sequences and a
common ancestor sequence during evolution.

8. Methods Of Sequence Alignment :
Alignment of Pairs of Sequences:
Alignment of two sequences is performed using
the following methods:
 Dot matrix analysis
 The dynamic programming (or DP)
algorithms
 Word or k-tuple methods, such as used by the
programs FASTA and BLAST,

9. DOT PLOT :
In Bioinformatics a dot plot is a graphical method that
allows the comparison of two biological sequences and
identify regions of close similarity between Them
Method for comparing two amino acid or nucleotide
sequences
Established in 1970 by A.J. Gibbs and G. A. McIntyre
Dot plots are useful as a first-level filter for determining
an alignment between two sequences.
It reveals the presence of insertions or deletions

10. DOT PLOT :
Principle:
 Dot plot are two dimensional graphs, showing a Comparison Between of two sequences. 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
Example:
Seq 1: GCTGAA
Seq 2: GCGAA
G C T G A A
G
C
T
A
A

11. DOT PLOT :
Dot Plot Algorithm :
 A dot plot is a visual representation of the similarities between two sequences.
One sequence (A) is listed across the top of the matrix and the other (B) is listed
down the left side
 Starting from the first character in B, one moves across the page keeping in the
first row and placing a dot in many column where the character in A is the same B
 The process is continued until all possible comparisons between A and B are made
 Any region of similarity is revealed by a Diagonal row of dots
 Isolated dots not on diagonal represent random matches.

12. DOT PLOT ALGORITHM :
Example:
Seq 1: TWILIGHTZONE
Seq 2: MIDNIGHTZONE
T W I L I G H T Z O N E
M
I
D
N
I
G
H
T
Z
O
N
Calculation: Matrix
• Rows = residues of sequence 1
• Column= residues of sequence 2.
A dot is plotted at every co-ordinate
where there is similarity between the
bases

13. EXAMPLES AND INTERPRETATIONS OF DOT PLOTS :
IDENTICAL SEQUENCE
DIRECT REPEAT
INVERTED REPEAT
PALINDROMIC SEQUENCES
LOW COMPLEXITY REGION
FRAME SHIFTS
WINDOW SIZE

14. IDENTICAL SEQUENCE:

15. DIRECT REPEAT:

16. INVERTED REPEAT:

17. PALINDROMIC SEQUENCES:

18. LOW COMPLEXITY REGION:

19. FRAME SHIFTS MUTATION:
What is frameshift mutation?
A Frameshift mutation (also called a framing error or a reading frame
shift) is a genetic mutation caused by indels (insertions or deletions) of a
number of nucleotides in a DNA sequence

20. Window Size :
DOT PLOT BECOMES TOO NOISY WHEN WE COMPARE LARGE AND SIMILAR
SEQUENCES:
 By using sliding window (size =w), cut-off (value=v)
 A residue by residue comparison (window size = 1) would undoubtedly result in a
very noisy background due to a lot of similarities between the two sequences of
interest. For DNA sequences the background noise will be even more dominant
as a match between only four nucleotide is very likely to happen. Moreover, a
residue by residue comparison (window size = 1) can be very time consuming and
computationally demanding.
 So Increase the Window Size
Window size changes with goal of
analysis
– size of average exon
– size of average protein structural
element
– size of gene promoter
– size of enzyme active site

21. Dot Plot Software:
GCG is a commercial software, hence not possible to use all the time.
Instead of this, we can use the EMBOSS package, which are followig:
 Dotmatcher
 Dotpath
 Polydot
 Dottup

22.  Shows the all possible alignment between two nucleic acid and amino acid sequences.
 All kind of local and global alignment can be traped .
 To find self base pairing of RNA (eg, tRNA) by comparing a sequence to itself
complemented and reverse.
 An excellent approach for finding sequence transposition.
 To find the location of genes between two genomes.
 Dot plot applications are particularly useful in the identification of interspersed repeats
such as transposons and tandem-repeat motifs such as microsatellites.
 Furthermore, loss or gain of whole motifs can easily be spotted in different types of
domains, a trait useful in characterising the evolution of certain protein families.
 Dot plots are also employed in the investigation of properties of protein coding
sequences by predicting secondary structures, like stem-loop formation or structural
RNA domains.
 Can use to find self base pairing of an RNA (e.g., tRNA) by comparing a sequence to
‐
itself complemented and reversed.
APPLICATION :

23. Comparing Two Protein sequence “Tubulin-specific chaperone A” B/w Human & Rabit

24. Out put
Tubulin-specific
chaperone
A
isoform
2
[Homo
sapiens]
Tubulin-specific chaperone A
Oryctolagus cuniculus (Rabbit)

25. Comparing Two Protein sequence “Filamin-A” B/W human & Rat

26. Out put

27. LIMITATION :
 For longer sequence, memory required for the graphical
representation is very high.
 So long sequence can not be aligned.
 Lots of Insignificant 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.
 i.e, Higher efficiency of short sequence.
 Low efficiency of long sequence.

28. THANK
YOU