Question: what is * in the NCBI Blosum and PAM matrices
0
gravatar for nobu.kim66
9 days ago by
nobu.kim6610
nobu.kim6610 wrote:
#  Matrix made by matblas from blosum45.iij
#  * column uses minimum score
#  BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 45
#  Entropy =   0.3795, Expected =  -0.2789
   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
A  5 -2 -1 -2 -1 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -2 -2  0 -1 -1  0 -5 
R -2  7  0 -1 -3  1  0 -2  0 -3 -2  3 -1 -2 -2 -1 -1 -2 -1 -2 -1  0 -1 -5 
N -1  0  6  2 -2  0  0  0  1 -2 -3  0 -2 -2 -2  1  0 -4 -2 -3  4  0 -1 -5 
D -2 -1  2  7 -3  0  2 -1  0 -4 -3  0 -3 -4 -1  0 -1 -4 -2 -3  5  1 -1 -5 
C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5 
Q -1  1  0  0 -3  6  2 -2  1 -2 -2  1  0 -4 -1  0 -1 -2 -1 -3  0  4 -1 -5 
E -1  0  0  2 -3  2  6 -2  0 -3 -2  1 -2 -3  0  0 -1 -3 -2 -3  1  4 -1 -5 
G  0 -2  0 -1 -3 -2 -2  7 -2 -4 -3 -2 -2 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -5 
H -2  0  1  0 -3  1  0 -2 10 -3 -2 -1  0 -2 -2 -1 -2 -3  2 -3  0  0 -1 -5 
I -1 -3 -2 -4 -3 -2 -3 -4 -3  5  2 -3  2  0 -2 -2 -1 -2  0  3 -3 -3 -1 -5 
L -1 -2 -3 -3 -2 -2 -2 -3 -2  2  5 -3  2  1 -3 -3 -1 -2  0  1 -3 -2 -1 -5 
K -1  3  0  0 -3  1  1 -2 -1 -3 -3  5 -1 -3 -1 -1 -1 -2 -1 -2  0  1 -1 -5 
M -1 -1 -2 -3 -2  0 -2 -2  0  2  2 -1  6  0 -2 -2 -1 -2  0  1 -2 -1 -1 -5 
F -2 -2 -2 -4 -2 -4 -3 -3 -2  0  1 -3  0  8 -3 -2 -1  1  3  0 -3 -3 -1 -5 
P -1 -2 -2 -1 -4 -1  0 -2 -2 -2 -3 -1 -2 -3  9 -1 -1 -3 -3 -3 -2 -1 -1 -5 
S  1 -1  1  0 -1  0  0  0 -1 -2 -3 -1 -2 -2 -1  4  2 -4 -2 -1  0  0  0 -5 
T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1  2  5 -3 -1  0  0 -1  0 -5 
W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2  1 -3 -4 -3 15  3 -3 -4 -2 -2 -5 
Y -2 -1 -2 -2 -3 -1 -2 -3  2  0  0 -1  0  3 -3 -2 -1  3  8 -1 -2 -2 -1 -5 
V  0 -2 -3 -3 -1 -3 -3 -3 -3  3  1 -2  1  0 -3 -1  0 -3 -1  5 -3 -3 -1 -5 
B -1 -1  4  5 -2  0  1 -1  0 -3 -3  0 -2 -3 -2  0  0 -4 -2 -3  4  2 -1 -5 
Z -1  0  0  1 -3  4  4 -2  0 -3 -2  1 -1 -3 -1  0 -1 -2 -2 -3  2  4 -1 -5 
X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1  0  0 -2 -1 -1 -1 -1 -1 -5 
* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5  1

What does the * mean?

pam blosum matrix • 92 views
ADD COMMENTlink written 9 days ago by nobu.kim6610

perhaps the star shows the penality when the letter codes do not match (and are not any of the valid aminoacids), perhaps a gap, just guess, but nice catch I've never noticed that line

ADD REPLYlink modified 8 days ago • written 8 days ago by Istvan Albert ♦♦ 85k

that's what I thought too, but maybe better to return some error message to the user in case that does happen (alongside any alignments)

ADD REPLYlink written 8 days ago by nobu.kim6610
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