NCBI C++ ToolKit
sm_pam250.c
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1 /* $Id: sm_pam250.c 30268 2006-09-25 19:30:59Z madden $
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information
6 *
7 * This software/database is a "United States Government Work" under the
8 * terms of the United States Copyright Act. It was written as part of
9 * the author's official duties as a United States Government employee and
10 * thus cannot be copyrighted. This software/database is freely available
11 * to the public for use. The National Library of Medicine and the U.S.
12 * Government have not placed any restriction on its use or reproduction.
13 *
14 * Although all reasonable efforts have been taken to ensure the accuracy
15 * and reliability of the software and data, the NLM and the U.S.
16 * Government do not and cannot warrant the performance or results that
17 * may be obtained by using this software or data. The NLM and the U.S.
18 * Government disclaim all warranties, express or implied, including
19 * warranties of performance, merchantability or fitness for any particular
20 * purpose.
21 *
22 * Please cite the author in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 * Author: Aaron Ucko, Mike Gertz
27 *
28 * File Description:
29 * Protein alignment score matrices; shared between the two toolkits.
30 *
31 * ===========================================================================
32 */
33 
35 
36 /** Entries for the PAM250 matrix at a scale of ln(2)/3.0. */
37 
38 static const TNCBIScore s_Pam250PSM[25 * 25] = {
39  /* A, R, N, D, C, Q, E, G, H, I, L, K, M,
40  F, P, S, T, W, Y, V, B, J, Z, X, * */
41  /*A*/ 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1,
42  -3, 1, 1, 1, -6, -3, 0, 0, -1, 0, -1, -8,
43  /*R*/ -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0,
44  -4, 0, 0, -1, 2, -4, -2, -1, -3, 0, -1, -8,
45  /*N*/ 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2,
46  -3, 0, 1, 0, -4, -2, -2, 2, -3, 1, -1, -8,
47  /*D*/ 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3,
48  -6, -1, 0, 0, -7, -4, -2, 3, -3, 3, -1, -8,
49  /*C*/ -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5,
50  -4, -3, 0, -2, -8, 0, -2, -4, -5, -5, -1, -8,
51  /*Q*/ 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1,
52  -5, 0, -1, -1, -5, -4, -2, 1, -2, 3, -1, -8,
53  /*E*/ 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2,
54  -5, -1, 0, 0, -7, -4, -2, 3, -3, 3, -1, -8,
55  /*G*/ 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3,
56  -5, 0, 1, 0, -7, -5, -1, 0, -4, 0, -1, -8,
57  /*H*/ -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2,
58  -2, 0, -1, -1, -3, 0, -2, 1, -2, 2, -1, -8,
59  /*I*/ -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2,
60  1, -2, -1, 0, -5, -1, 4, -2, 3, -2, -1, -8,
61  /*L*/ -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4,
62  2, -3, -3, -2, -2, -1, 2, -3, 5, -3, -1, -8,
63  /*K*/ -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0,
64  -5, -1, 0, 0, -3, -4, -2, 1, -3, 0, -1, -8,
65  /*M*/ -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6,
66  0, -2, -2, -1, -4, -2, 2, -2, 3, -2, -1, -8,
67  /*F*/ -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0,
68  9, -5, -3, -3, 0, 7, -1, -4, 2, -5, -1, -8,
69  /*P*/ 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2,
70  -5, 6, 1, 0, -6, -5, -1, -1, -2, 0, -1, -8,
71  /*S*/ 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2,
72  -3, 1, 2, 1, -2, -3, -1, 0, -2, 0, -1, -8,
73  /*T*/ 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1,
74  -3, 0, 1, 3, -5, -3, 0, 0, -1, -1, -1, -8,
75  /*W*/ -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4,
76  0, -6, -2, -5, 17, 0, -6, -5, -3, -6, -1, -8,
77  /*Y*/ -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2,
78  7, -5, -3, -3, 0, 10, -2, -3, -1, -4, -1, -8,
79  /*V*/ 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2,
80  -1, -1, -1, 0, -6, -2, 4, -2, 2, -2, -1, -8,
81  /*B*/ 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2,
82  -4, -1, 0, 0, -5, -3, -2, 3, -3, 2, -1, -8,
83  /*J*/ -1, -3, -3, -3, -5, -2, -3, -4, -2, 3, 5, -3, 3,
84  2, -2, -2, -1, -3, -1, 2, -3, 5, -2, -1, -8,
85  /*Z*/ 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2,
86  -5, 0, 0, -1, -6, -4, -2, 2, -2, 3, -1, -8,
87  /*X*/ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
88  -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -8,
89  /***/ -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
90  -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, 1
91 };
93  "ARNDCQEGHILKMFPSTWYVBJZX*",
95  -8
96 };
97 
int TNCBIScore
data types
Definition: raw_scoremat.h:45
const SNCBIPackedScoreMatrix NCBISM_Pam250
Definition: sm_pam250.c:92
static const TNCBIScore s_Pam250PSM[25 *25]
Entries for the PAM250 matrix at a scale of ln(2)/3.0.
Definition: sm_pam250.c:38
Modified on Sun Jul 21 04:21:51 2024 by modify_doxy.py rev. 669887