Introduction to bioinformatics: Distance measure between two biological sequences (edit distance and hamming distance

1. DISTANCE MEASURE
BETWEEN TWO
BIOLOGICAL
SEQUENCES
Shweta Kumari
M. Sc. Bioinformatics
1st
semester
Roll no. - 21

2. 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

3. 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

4. HAMMING DISTANCE
Hamming 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.

5. EXAMPLE OF HAMMING
DISTANCE
ATCGGTAGT
ATGGTTCCT
The hamming distance between these two
sequences is 4.

6. 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.

7. 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.

8. 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.

9. EXAMPLE OF EDIT
DISTANCE
ATGCA
T CA
Minimum no. of edit operation = 2

10. 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.

11. REFERENCES
http://www.maths.manchester.ac.uk/~pas/code/not
es/part2.pdf
 http://en.wikipedia.org/wiki/Hamming_distance
http://schatzlab.cshl.edu/teaching/2011/2011.Lectu
re3.Sequence%20Alignment.pdf
https://www.princeton.edu/~achaney/tmve/wiki100
k/docs/Hamming_distance.html
http://en.wikipedia.org/wiki/Edit_distance

12. THANK
YOU