Question

In: Computer Science

Problem: Given seven 8-mers as listed below ATCGATAG GGCCAATT CGATATCG AAGCAAGC AGCGTACG CCGCATTA ATCCATCG 1) Create...

Problem: Given seven 8-mers as listed below

ATCGATAG

GGCCAATT

CGATATCG

AAGCAAGC

AGCGTACG

CCGCATTA

ATCCATCG

1) Create the profile matrix; 2) Derive the consensus; 3) Calculate the consensus score; 4) Calculate the total distance between the 8-mers and the consensus.

Solutions

Expert Solution

Solution for the question is provided below. Please comment if any doubt below.

  1. Profile Matrix

The profile matrix is the count of each nucleotide base in the sequence. The sequence given is,

ATCGATAG

GGCCAATT

CGATATCG

AAGCAAGC

AGCGTACG

CCGCATTA

ATCCATCG

The profile matrix for the corresponding sequence is provided below.

A

4

1

1

0

6

3

1

1

C

2

1

4

4

0

0

3

1

G

1

3

2

2

0

0

1

4

T

0

2

0

1

1

4

2

1

  1. Consensus

Consensus can be found by find the nucleotide that has maximum count in each position.   

A

4

1

1

0

6

3

1

1

C

2

1

4

4

0

0

3

1

G

1

3

2

2

0

0

1

4

T

0

2

0

1

1

4

2

1

Consensus

A

G

C

C

A

T

C

G

Therefore the consensus is AGCCATCG

  1. Consensus Score

Consensus score can be found by calculating the sum of count of each nucleotide in the consensus.

A

4

1

1

0

6

3

1

1

C

2

1

4

4

0

0

3

1

G

1

3

2

2

0

0

1

4

T

0

2

0

1

1

4

2

1

Score = 4+3+4+4+6+4+3+4 =32

  1. Total Distance

Total Distance can be calculated by the sum of count of different nucleotide in each position on comparing with consensus.

A

4

1

1

0

6

3

1

1

C

2

1

4

4

0

0

3

1

G

1

3

2

2

0

0

1

4

T

0

2

0

1

1

4

2

1

2+1=3

1+1+2=4

1+2=3

2+1=3

1

3

1+1+2=4

1+1+1=3

Total distance =3+4+3+3+1+3+4+3 =24

venereology answered 1 day ago
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