Portein Sequence Alignment Question: Can someone tell me how you came to the con

Question

Portein Sequence Alignment Question:

Can someone tell me how you came to the conclusion that the score used for the Gap Penalty. IF you can also show me how this is done with matrices that would nice as well:

Teacher gave a Gap Penalty model where: Wn = G0 + N * G1

Thanks!

15) The protein sequence alignment shown below has a total score of 28. Knowing that the score for an exact match is 5 and the score for a mismatch is -4, what is the score used for the (constant, i.e. independent of length) gap penalty: GCTGGAAG-GCA-T GC- AGAGCACT A)-1 B)-2 C)-3 D)-4 E) Undefined (any value would give the same total score) Total score = 28 = 5*8 +3*x-> x = (28-40)/3--4 (it was important to notice that the cost of a gap is independent of its length, as said explicitly in the text of the question; there are therefore 3 gaps to consider, it does not matter that there are 6 residues total in those gaps)

Explanation / Answer

In this context, we have to use Gap Penalty model where: Wn = G0 + N * G1

That means, we have to include gap opening penalty (G0) and gap extension penalty (G1) and N is the length of the total Gap

GCTGGAAG-GC A -T

GC- - - - AGAGCACT

Then total score= (5*8) + (6*x)

28 = 40 + 6x

- 12 = 6x

x= -2

then the gap penalty score will be -2

Related Questions

Navigate

• Browse (All)
• Browse P
• Subjects

---