LECTURE 3

Selected Topics in
Computer
Science
CS409 Introduction To
bioinformatics
DR. Ashraf Hendam
OUTLINE
• Calculation of sequence similarity/Identity
• What is Sequence alignment
• Why sequence alignment
• Sequence alignment terms
• Sequence alignment Types
Pairwise sequence alignment
Global and Local Alignment
Local alignment
Why Local alignment
Local alignment Example
Global alignment
Global alignment example
Global and. Local comparison
Multiple sequence alignment
• Pairwise alignment implementation
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Calculation of sequence similarity/Identity

Calculation of sequence similarity/Identity for two

sequences of equal length

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Calculation of sequence similarity/Identity

Calculation of sequence similarity/Identity for two

sequences of non equal length
I(S)= (Li(s)/Ly)* 100
Where
Li(s) is the number of aligned residues with similar
or identical characteristics
Ly is the length of the shorter of the two
sequences
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Similarity and Identity Example

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Back
Amino Acids Similarity and Identity
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
M A R N D C E Q G H I L K F P S T W Y V
M G R N E C E Q G H I L R F P S

Identity=(13/16)*100=81.25%
Similarity= (16/16)*100=100%
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

M A R N D C E Q G H I L K F P S T W Y V

M G R N E C E Q G H I L R F P S S W Y V

Identity=(16*2)/(20+20)*100=80%
Similarity=(20*2)/(20+20)*100=100%
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What is Sequence alignment

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What is Sequence alignment

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What is Sequence alignment

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What is Sequence alignment

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What is Sequence alignment

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Back
Why sequence alignment

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Why sequence alignment

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Why sequence alignment

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Sequence alignment terms

• Match=the same nucleotide appears in both sequences.

• Mismatch=different nucleotides are found in the two sequences.
• Gaps= a base in one sequence and a null base in the other.
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Sequence alignment terms

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Sequence alignment terms

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Sequence alignment terms

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Sequence alignment Types
Number of compared sequences
Pairwise alignment
Local alignment
Global alignment
Multiple Alignment

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Pairwise sequence alignment

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Pairwise sequence alignment
• The process of lining up two sequences to achieve
maximal levels of identity (and conservation, in the
case of amino acid sequences) for the purpose of
assessing the degree of similarity and the
possibility of homology.
• Pairwise sequence alignment is the most
fundamental operation of bioinformatics.

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Pairwise sequence alignment

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Global and Local Alignment
• Local Alignment
–An “internal” alignment or embedding of a
substring (sic) into a target string
• Global Alignment
–Every character in the query (source) string
lines up with a character in the target string
–May require gap (space) insertion to make
strings the same length
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Local alignment

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Why Local alignment

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Local alignment Example

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Global alignment

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Global alignment example

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Global and Local comparison

Back

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Back
Multiple sequence alignment

• Conserved domain analysis

• Primer Designing

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Back
Pairwise alignment implementation

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Pairwise alignment implementation

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Pairwise alignment implementation
Dot Matrix
• Is a two-dimensional array of dots used to highlight
the exact matches between two sequences.Given two
sequences A = a1a2 …am and B = b1b2 …bn .
• A dot is plotted on the (i, j) entry of the matrix if ai =
bj
• Users can easily identify similar regions between the
two sequences by locating those contiguous dots
along the same diagonal.

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Pairwise alignment implementation
Using dot matrix align two the following sequences:
GTACGTCGG
ATACATGTCT
G T A C G T C G G

A
T
TAC
A GTC
C
A
T
G
T
C
T
Pairwise alignment implementation
TTCTAT
TCTAAC
ATTCTA
TCTA
CTA
CTA

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Pairwise alignment implementation

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Pairwise alignment implementation

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Pairwise alignment implementation

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