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Local and Global Sequence Alignment 5+5 Examples

Md. Abdullah completed assignment 01 which involved 5 examples of global and local sequence alignment problems. For the global alignments, the Needleman-Wunsch algorithm was used to create a 2D matrix, trace back the optimal path, and output the final alignment. For the local alignments, the Smith-Waterman algorithm followed the same three steps. Each example provided the sequences, scoring scheme, and solution 2D matrix to find the optimal local or global alignment.

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144 views10 pages

Local and Global Sequence Alignment 5+5 Examples

Md. Abdullah completed assignment 01 which involved 5 examples of global and local sequence alignment problems. For the global alignments, the Needleman-Wunsch algorithm was used to create a 2D matrix, trace back the optimal path, and output the final alignment. For the local alignments, the Smith-Waterman algorithm followed the same three steps. Each example provided the sequences, scoring scheme, and solution 2D matrix to find the optimal local or global alignment.

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mdabdullah mdabdullah
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Name : Md.

Abdullah
ID : IT-17015
Assignment no: 01
Name of the assignment: Local and global sequence alignments 5+5 examples.
Global sequence alignment:
Global alignments, which attempt to align every residue in every sequence, are most useful when
the sequences in the query set are similar and of roughly equal size.
Algorithm used:

 Needleman-wunsch
Needleman-wunsch algorithm: three major steps, these are:
 Create 2D Matrix
 Trace back
 Final Alignment

Example 1: Find the final sequence for the following problems


Given, sequence1=GGGC, sequence2=GTC, match=1, mismatch= -1, gap= -2.
Ans:

G T C

0 -2 -4 -6

G -2 1 -4 -3 -6 -5 -8
-
4 1 -1 -1 -3 -3
G -4 -1 -1 0 -3 -2 -5

-6 -1 -3 0 -2 -2
G -6 -3 -3 -2 -2 -1 -4

-8 -3 -5 -2 -4 -1
C -8 -7 -5 -4 -4 -1 -3

-10 -5 -7 -4 -6 -1
Final alignment:
GTC
GGGC

Example 2: Find the final sequence for the following problems


Given, sequence1=GCAT, sequence2=GATT, match=1, mismatch= -1, gap= -1

G C A T

0 -1 -2 -3 -4

G -1 1 -2 -2 -3 --3 -4 -4 -5

-2 1 0 0 -1 -1 -2 -2
A -2 -2 0 0 -1 1 -2 -2 -3

-3 0 -1 0 -1 1 0 0
T -3 -3 -1 -1 -1 -1 0 2 -1

-4 -1 -2 -1 -2 0 -1 2
T -4 -4 -2 -2 -2 -2 -1 1 -1

-5 -2 -3 -2 -3 -1 -2 1

Final alignment:
GCAT
GATT
Example 3:
Find the final sequence for the following problems
Given, sequence1=ACA, sequence2=AATA, match=1, mismatch= -1, gap= -1

Ans:

A C A

0 -1 -2 -3

A -1 1 -2 -2 -3 --3 -4

-2 1 0 0 -1 -1
A -2 -2 0 0 -1 1 -2

-3 0 -1 0 -1 1
T -3 -3 -1 -1 -1 -1 0

-4 -1 -2 -1 -2 0
T -4 -4 -2 -2 -2 -2 -1

-5 -2 -3 -2 -3 -1

Final alignments:
A C -A
AATT
Example 4: Find the final sequence for the following problems
Given, sequence1=ACAA, sequence2=ACTGA, match=1, mismatch= -1, gap= -1

Ans:

A C A A

0 -1 -2 -3 -4

A -1 1 -2 -2 -3 --1 -4 -2 -5

-2 1 0 0 -1 -1 -2 -2
C -2 -2 0 2 -1 -1 -2 -2 -3

-3 0 -1 2 -1 -1 -2 -2
T -3 -3 -1 -1 -1 -1 -2 -2 -3

-4 -1 -2 -1 -2 -1 -2 -2
G -4 -4 -2 -2 -2 -2 -2 -2 -3

-5 -2 -3 -2 -3 -2 -3 -2

A -5 -3 -3 -3 -3 -1 -3 -1 -3

-6 -3 -4 -3 -4 -1 -2 -1

Final alignment:
ACAA
ACTGA
Example 5:
Find the final sequence for the following problems
Given, sequence1=ACAA, sequence2=ACTGA, match=1, mismatch= -1, gap= -1
Ans:

G C A T G

0 -1 -2 -3 -4 -5

G -1 1 -2 -2 -3 --3 -4 -4 -5 -3 -6

-2 1 0 0 -1 -1 -2 -2 -3 -3
A -2 -2 0 0 -1 1 -2 -2 -3 -3 -4

-3 0 -1 0 -1 1 0 0 -1 -1
T -3 -3 -1 -1 -1 -1 0 2 -1 -1 -2

-4 -1 -2 -1 -2 0 -1 2 -1 -1
T -4 -4 -2 -2 -2 -2 -1 1 1 1 -2

-5 -2 -3 -2 -3 -1 -2 1 0 0

A -5 -5 -3 -3 -3 -1 -2 -2 0 0 -1

-6 -3 -4 -3 -4 -1 -2 0 -1 0
C -6 -6 -4 -2 -4 -4 -2 -2 -1 -1 -1

-7 -4 -5 -2 -3 -2 -3 -1 -2 -1

Final alignment:
GC-ATG
GATTAC
Local Alignment:

 Local alignment program is based on Simth-Waterman algorithm.


 Suitable for partially similar, different length and conserved region containing sequences
Smith-Waterman algorithm:
There are three steps in smith-waterman algorithm:
 Create 2D matrix
 Trace back
 Final Alignment.
Example 1: Find the final sequence for the following problems
Given, sequence1=GGGC, sequence2=GTC, match=1, mismatch= -1, gap= -1
Ans:

G T C

0 0 0 0

G 0 1 -1 -1 -1 -1 -1

-1 1 0 0 -1 0
G 0 1 0 0 -1 -1 -1

-1 1 -1 0 -1 0
G 0 1 0 -1 -1 -1 -1

-1 1 0 0 -1 0
C 0 -1 0 0 -1 -1 -1

-1 0 -1 0 -1 0

Final alignment:
-GTC
GGGC
Example 2: Find the final sequence for the following problems
Given, sequence1=GCAT, sequence2=GATT, match=1, mismatch= -1, gap= -2

G G T T

0 0 0 0 0

G 0 1 -2 1 -2 --1 -2 -1 -2

-2 1 -1 1 -1 0 -2 0
A 0 -1 -1 0 -1 0 -2 -1 -2

-2 0 -2 0 -2 0 -2 0
T 0 -1 -2 -1 -2 1 -2 1 -2

-2 0 -2 0 -2 1 -1 1
T 0 -1 -2 -1 -2 1 -2 2 -1

-2 0 -2 0 -2 1 -1 2

Final alignment:
GGTT
GATT
Example 3: Find the final sequence for the following problems
Given, sequence1=GAATT, sequence2=GGTTC, match=1, mismatch= -1, gap= -2.
Ans:

G A G T C

0 0 0 0 0 0

G 0 1 -2 -1 -2 1 -2 -1 -2 -1 -2

-2 1 -1 0 -2 1 -1 0 -2 0
C 0 -1 -1 0 -2 -1 -1 0 -2 1 -2

-2 0 -2 0 -2 0 -2 0 -2 1
A 0 -1 -2 1 -2 -1 -2 -1 -2 -1 -1

-2 0 -2 1 -1 0 -2 0 -2 0
T 0 -1 -2 -1 -1 0 -2 1 -2 -1 -2

-2 0 -2 0 -2 0 -2 0 -2 0

T 0 -1 -2 -1 -2 -1 -2 1 -2 -1 -2

-2 0 -2 0 -2 0 -2 1 -1 0

Final alignment:
GAGTC
GCATT
Example 4: Find the final sequence for the following problems
Given, sequence1=GGGT, sequence2=GGA, match=1, mismatch= -1, gap= -2.

Ans:

G G A

0 0 0 0

G 0 1 -2 1 -2 -1 -2

-2 1 -2 1 -2 0
G 0 1 -1 2 -1 0 -2

-2 1 -2 2 0 0
G 0 1 -1 2 0 1 -2

-2 1 -1 2 0 1
T 0 -1 -1 0 0 1 -1

-2 0 -2 0 -2 1

Final alignment:
-GGA
GGGT
Example 5: Find the final sequence for the following problems
Given, sequence1=AGGT, sequence2=AGGA, match=1, mismatch= -1, gap= -2.

Ans:

A G G T

0 0 0 0 0

A 0 1 -2 -1 -2 -1 -2 -1 -2

-2 1 -1 0 -2 0 -2 0
G 0 1 -1 2 -2 1 -2 -1 -2

-2 1 -1 2 0 1 -1 0
G 0 -1 -1 2 0 3 -2 0 -2

-2 0 -2 2 0 3 1 1
A 0 1 -2 -1 0 1 1 2 -1

-2 1 -1 0 -2 1 -1 2

Final alignment:
AGGT
AGGA

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