DOT MATRIX ANALYSIS

This is a graphical method

Primarily used for finding regions of local matches between sequences

Introduced by Gibbs and McIntyre in 1970.

It’s a very simple method.

The two sequences to be compared are placed as the rows and columns of a matrix.

Then the residues are compared and a dot is plotted at every point where a match is found.

A modification to the above method is suggested. Instead of looking for a match at every residue, some amount of match in every successive overlapping window of residues sought. Usually for DNA the window is of 11 residues is ought with at least 7 matches and for proteins sequences a window of 3 residues with minimum 2 matches are considered. This kind of smoothening procedure leads to a plot with dots representing only significant matches.

Ther e are a number of programs available for DOT Matrix Analyses like : DOTTER, DOTLET, PALIGN.

A number of alignments are possible by using a DOT Matrix Plot. We have to get an optimum alignment for these plots.

Dot matrix Technique is developed in 3 stages

1) Residue to Residue Matching

There are certain disadvantages with this:

a) Signal – noise ratio is low

Signal means visual pattern on the graph

b) The chance of random match is high

So the technique is improved by the use of words or oligimers.

2) Use of words

Advantages : this method decreased the chance of random match.

Disadvantages : when the length of the word is too long then the number of dots decreases as there is low probability that a given word matches in between two sequences.

3) Use of windows

Instead of words or oligomers we here use windows. For protein sequences a window should have 3 residues and for nucleotide sequences a window has 11 residues.

With in a window we set a minimum number of matches.

This method has the advantage of decreasing the chance of random match and at the same time overcomes the disadvantage associated with using words/oligomers.