Add PAM10 substitution score matrix default tip
authorMartin C. Frith
Wed Oct 09 19:22:22 2019 +0900 (6 weeks ago)
changeset 992e57e547b8235
parent 991 7f841cc97f20
Add PAM10 substitution score matrix
data/BL80.mat
data/PAM10.mat
data/PAM30.mat
     1.1 --- a/data/BL80.mat	Tue Oct 08 19:21:37 2019 +0900
     1.2 +++ b/data/BL80.mat	Wed Oct 09 19:22:22 2019 +0900
     1.3 @@ -1,5 +1,5 @@
     1.4 -# This protein scoring scheme is good at finding somewhat
     1.5 -# short-and-strong similarities.  (S Henikoff & JG Henikoff, PNAS 1992
     1.6 +# This protein scoring scheme is good for finding somewhat strong, and
     1.7 +# short, similarities.  (S Henikoff & JG Henikoff, PNAS 1992
     1.8  # 89(22):10915-9).
     1.9  
    1.10  #nickname BLOSUM80
     2.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     2.2 +++ b/data/PAM10.mat	Wed Oct 09 19:22:22 2019 +0900
     2.3 @@ -0,0 +1,29 @@
     2.4 +# This protein scoring scheme is good for finding very strong, and
     2.5 +# short, similarities (MO Dayhoff et al. 1978).
     2.6 +
     2.7 +#last -a20 -b3
     2.8 +    A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
     2.9 +A   7 -10  -7  -6 -10  -7  -5  -4 -11  -8  -9 -10  -8 -12  -4  -3  -3 -20 -11  -5  -6  -6  -6 -23
    2.10 +R -10   9  -9 -17 -11  -4 -15 -13  -4  -8 -12  -2  -7 -12  -7  -6 -10  -5 -14 -11 -11  -7  -9 -23
    2.11 +N  -7  -9   9  -1 -17  -7  -5  -6  -2  -8 -10  -4 -15 -12  -9  -2  -5 -11  -7 -12   7  -6  -6 -23
    2.12 +D  -6 -17  -1   8 -21  -6   0  -6  -7 -11 -19  -8 -17 -21 -12  -7  -8 -21 -17 -11   7  -1  -9 -23
    2.13 +C -10 -11 -17 -21  10 -20 -20 -13 -10  -9 -21 -20 -20 -19 -11  -6 -11 -22  -7  -9 -18 -20 -13 -23
    2.14 +Q  -7  -4  -7  -6 -20   9  -1 -10  -2 -11  -8  -6  -7 -19  -6  -8  -9 -19 -18 -10  -6   7  -8 -23
    2.15 +E  -5 -15  -5   0 -20  -1   8  -7  -9  -8 -13  -7 -10 -20  -9  -7  -9 -23 -11 -10  -1   7  -8 -23
    2.16 +G  -4 -13  -6  -6 -13 -10  -7   7 -13 -17 -14 -10 -12 -12 -10  -4 -10 -21 -20  -9  -6  -8  -8 -23
    2.17 +H -11  -4  -2  -7 -10  -2  -9 -13  10 -13  -9 -10 -17  -9  -7  -9 -11 -10  -6  -9  -4  -4  -8 -23
    2.18 +I  -8  -8  -8 -11  -9 -11  -8 -17 -13   9  -4  -9  -3  -5 -12 -10  -5 -20  -9  -1  -9  -9  -8 -23
    2.19 +L  -9 -12 -10 -19 -21  -8 -13 -14  -9  -4   7 -11  -2  -5 -10 -12 -10  -9 -10  -5 -12 -10  -9 -23
    2.20 +K -10  -2  -4  -8 -20  -6  -7 -10 -10  -9 -11   7  -4 -20 -10  -7  -6 -18 -12 -13  -5  -6  -8 -23
    2.21 +M  -8  -7 -15 -17 -20  -7 -10 -12 -17  -3  -2  -4  12  -7 -11  -8  -7 -19 -17  -4 -16  -8  -9 -23
    2.22 +F -12 -12 -12 -21 -19 -19 -20 -12  -9  -5  -5 -20  -7   9 -13  -9 -12  -7  -1 -12 -14 -20 -12 -23
    2.23 +P  -4  -7  -9 -12 -11  -6  -9 -10  -7 -12 -10 -10 -11 -13   8  -4  -7 -20 -20  -9 -10  -7  -8 -23
    2.24 +S  -3  -6  -2  -7  -6  -8  -7  -4  -9 -10 -12  -7  -8  -9  -4   7  -2  -8 -10 -10  -4  -8  -6 -23
    2.25 +T  -3 -10  -5  -8 -11  -9  -9 -10 -11  -5 -10  -6  -7 -12  -7  -2   8 -19  -9  -6  -6  -9  -7 -23
    2.26 +W -20  -5 -11 -21 -22 -19 -23 -21 -10 -20  -9 -18 -19  -7 -20  -8 -19  13  -8 -22 -13 -21 -16 -23
    2.27 +Y -11 -14  -7 -17  -7 -18 -11 -20  -6  -9 -10 -12 -17  -1 -20 -10  -9  -8  10 -10  -9 -13 -11 -23
    2.28 +V  -5 -11 -12 -11  -9 -10 -10  -9  -9  -1  -5 -13  -4 -12  -9 -10  -6 -22 -10   8 -11 -10  -8 -23
    2.29 +B  -6 -11   7   7 -18  -6  -1  -6  -4  -9 -12  -5 -16 -14 -10  -4  -6 -13  -9 -11   7  -3  -8 -23
    2.30 +Z  -6  -7  -6  -1 -20   7   7  -8  -4  -9 -10  -6  -8 -20  -7  -8  -9 -21 -13 -10  -3   7  -8 -23
    2.31 +X  -6  -9  -6  -9 -13  -8  -8  -8  -8  -8  -9  -8  -9 -12  -8  -6  -7 -16 -11  -8  -8  -8  -8 -23
    2.32 +* -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23   1
     3.1 --- a/data/PAM30.mat	Tue Oct 08 19:21:37 2019 +0900
     3.2 +++ b/data/PAM30.mat	Wed Oct 09 19:22:22 2019 +0900
     3.3 @@ -1,4 +1,4 @@
     3.4 -# This protein scoring scheme is good for finding short-and-strong
     3.5 +# This protein scoring scheme is good for finding strong, and short,
     3.6  # similarities (MO Dayhoff et al. 1978).
     3.7  
     3.8  #last -a13 -b3