DISTANCE MEASURE BETWEEN TWO

BIOLOGICAL SEQUENCES

Shweta KumariM. Sc. Bioinformatics1st semesterRoll no. - 21

CONTENT

INTRODUCTION HAMMING DISTANCE EXAMPLE OF HAMMING DISTANCE LIMITATIONS OF HAMMING DISTANCE EDIT DISTANCE RULES FOR EDIT DISTANCE EXAMPLE OF EDIT DISTANCE HAMMING DISTANCE V/S EDIT DISTANCE REFERENCES

INTRODUCTION It is the measure of distance between sequences, which allow us to infer their similarities and related biological functions.

The distance measure due to similarities suggest us homology between the sequences.

It also help us to know the evolutionary relationship.

Distance can be calculated by these methods – Hamming distance Edit distance

HAMMING DISTANCEHamming distance is the measure of dissimilarity between two sequences i.e, the no. of positions at which the corresponding character are different.

It measure the minimum no. of substitutions required to change one character into the other.

It was introduced by RICHARD HAMMING in 1950.

EXAMPLE OF HAMMING DISTANCE

ATCGGTAGT ATGGTTCCT The hamming distance between these two sequences is 4.

LIMITATIONS OF HAMMING DISTANCE

Both the sequences having same length.

Two sequences of unequal length having high similarity will fail to align.

We can’t perform edit operation on any sequences.

Distance calculation of two sequences having unequal length can be measured by an alternative way called EDIT DISTANCE.

EDIT DISTANCE Similarity between two sequences as minimum no. of edit operation ( substitution, insertion & deletion ) needed to transform one to other.

Also called LEVENSHTEIN DISTANCE, developed by VLADIMIR LEVENSHTEIN in 1966.

It gives an indication of how close two sequences are, which are applicable for various purpose-

To find gene or protein that may have shared functions or properties.

To infer family relationship & evolutionary tress over different organism.

RULES FOR EDIT DISTANCE

Edit operation (substitution & indel ) must be performed on only one sequence.

It must not affect the length of the sequence.

Every character or gap of first sequence should be align with every character or gap of other sequence.

EXAMPLE OF EDIT DISTANCE

ATGCA T CA

Minimum no. of edit operation = 2

HAMMING DISTANCE V/S EDIT DISTANCE

Unlike hamming distance, edit distance allow us to compare sequences of different length.

Hamming distance is a simple position by position comparision while edit distance is formalised through insertion and deletion operation.

REFERENCEShttp://www.maths.manchester.ac.uk/~pas/code/notes/part2.pdf

http://en.wikipedia.org/wiki/Hamming_distance

http://schatzlab.cshl.edu/teaching/2011/2011.Lecture3.Sequence%20Alignment.pdf

https://www.princeton.edu/~achaney/tmve/wiki100k/docs/Hamming_distance.html

http://en.wikipedia.org/wiki/Edit_distance

THANK YOU