dot plot analysis

Algorithm in bioinformatics : DOT PLOT analysis

1. Dot plot interpretationDot plot interpretation
Submitted by:
Shweta Kumari
Roll no: 21
M.Sc Bioinformatics
2nd semester
Session: 2014-16

2. ContentContent

Introduction

Principle

Example

Dot plot interpretation

Analysis of dot plot matrix

Identical sequence

Direct repeat

Inverted repeat

Palindromic sequence

Frame shifts

Low complexity region

Application

Limitation

Dot plot software

References

3. IntroductionIntroduction

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.

Introduced by GIBBS and MCLNTYE in 1970.

It is the one way to visualize that similarity between two
protein and nucleotide sequences by uses a similarity matrix.

4. PrinciplePrinciple

Dot plot are two dimensional graphs, showing a comarision 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.

Calculation:
Matrix
• Columns = residues of sequence 1
• Rows = residues of sequence 2

A dot is plotted at every co-ordinate where there is similarity between the bases.

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

6. Dot plot interpretationDot plot interpretation
Seq1: ATGATAT
Seq2: ATGATAT

7. Analysis of dot plot matrixAnalysis of dot plot matrix

Region of similarity appears as diagonal run of dots.

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.

8. Identical sequenceIdentical sequence

These are the two identical sequences:

Seq1: MALWGRL

Seq2: MALWGRL

9. Direct repeatDirect repeat

10. Inverted repeatInverted repeat
An inverted repeat is sequence of nucleotides followed downstream by its
reverse complement.
Inverted repeat: abcdeedcbafghijklmno

11. Palindromic sequencesPalindromic sequences
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.

12. Frame shiftsFrame shifts
Frame shifts in a nucleotide
sequence can occur due to
insertions, deletions or
mutations.
1. Deletion of nucleotides
2.Insertion of nucleotides
3.Mutation (out of frame)

13. Low cmplexity regionLow cmplexity region

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 [Wootton and Federhen,1993].

14. ApplicationApplication

Shows the all possible alignment between two nucleic acid
and amino acid sequences.

All kind of local and global aligment can be traped.

Help to recognise large region of simiarity.

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.

To find the non sequential alignment.

15. LimitationLimitation

For longer sequence, memory required for the graphical
representation is very high. So long sequnece can not be
aligned.

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 squences time of the search
window.

i.e, higher efficiency of short sequence.

Low efficiency of long sequence.

16. Dot plot softwareDot 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
(http://emboss.bioinformatics.nl/cgi-bin/emboss/dottup)

17. ReferencesReferences
●
Bioinformatics Principal and Applications by Zhumur Ghosh
and Bibekanand Mallick
●
Bioinformatics concepts, skill & applications, second edition by
S.C.Rastogi, Namita Mendriatta, Parag Rastogi

http://en.wikipedia.org/wiki/Dot_plot_%28bioinformatics%29

http://www.code10.info/index.php?option=com_content&view=ar
ticle&id=64:inroduction-to-dot-plots&catid=52:cat_coding_al
gorithms_dot-plots&Itemid=76

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