Question: Calculating Pairwise Alignment Scores
0
gravatar for imrbayil
5 days ago by
imrbayil0
imrbayil0 wrote:

I have exam for bioinformatic.I could understand globol algorithm and local algorithm.but ı have a problem gap opening penalty and gap extension penalty.What is the exactly different between gap opening penalty and gap extension? Can anybody help me how to use gap opening penalty and gap extension penalty for blosum62. there are a lot of questions like below.

Compute the score of the following sequence alignment given the BLOSUM62 matrix below and gap opening penalty (GOP) = 12, and gap extension penalty (GEP) = 2 .
SDRVIKAAIFDPIQPDF---G-----PVYFGLGHVH
RDLVERLFILDMI-PGLIKAGDSFPIPVALMINHIF

A R N D C Q E G H I L K M F P S T W Y V
A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0
R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3
N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3
D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3
C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1
Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2
E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2
G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3
H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3
I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3
L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1
K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2
M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1
F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2
S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2
T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3
Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1
V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4
pairwise alignment blosum • 55 views
ADD COMMENTlink modified 5 days ago by Benn7.9k • written 5 days ago by imrbayil0
0
gravatar for Benn
5 days ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

Gap opening penalty, is the number of points you'll have to subtract when a gap starts (12 in your case with blosum62), and extension penalty is when the gap extents further after opening (so each additional gap after the first opening one). When a gap closes and a new gap opens, you'll get a new opening penalty, etc.

Read more about alignment if this doesn't make sense, it is pretty much essential information of how alignment works namely.

If there is no textbook, try to find some stuff from internet, like here for example.

ADD COMMENTlink modified 5 days ago • written 5 days ago by Benn7.9k
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