NCBI C++ ToolKit
sm_pam30.c
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1 /* $Id: sm_pam30.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 PAM30 matrix at a scale of ln(2)/2.0. */
37 
38 static const TNCBIScore s_Pam30PSM[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*/ 6, -7, -4, -3, -6, -4, -2, -2, -7, -5, -6, -7, -5,
42  -8, -2, 0, -1,-13, -8, -2, -3, -6, -3, -1,-17,
43  /*R*/ -7, 8, -6,-10, -8, -2, -9, -9, -2, -5, -8, 0, -4,
44  -9, -4, -3, -6, -2,-10, -8, -7, -7, -4, -1,-17,
45  /*N*/ -4, -6, 8, 2,-11, -3, -2, -3, 0, -5, -7, -1, -9,
46  -9, -6, 0, -2, -8, -4, -8, 6, -6, -3, -1,-17,
47  /*D*/ -3,-10, 2, 8,-14, -2, 2, -3, -4, -7,-12, -4,-11,
48  -15, -8, -4, -5,-15,-11, -8, 6,-10, 1, -1,-17,
49  /*C*/ -6, -8,-11,-14, 10,-14,-14, -9, -7, -6,-15,-14,-13,
50  -13, -8, -3, -8,-15, -4, -6,-12, -9,-14, -1,-17,
51  /*Q*/ -4, -2, -3, -2,-14, 8, 1, -7, 1, -8, -5, -3, -4,
52  -13, -3, -5, -5,-13,-12, -7, -3, -5, 6, -1,-17,
53  /*E*/ -2, -9, -2, 2,-14, 1, 8, -4, -5, -5, -9, -4, -7,
54  -14, -5, -4, -6,-17, -8, -6, 1, -7, 6, -1,-17,
55  /*G*/ -2, -9, -3, -3, -9, -7, -4, 6, -9,-11,-10, -7, -8,
56  -9, -6, -2, -6,-15,-14, -5, -3,-10, -5, -1,-17,
57  /*H*/ -7, -2, 0, -4, -7, 1, -5, -9, 9, -9, -6, -6,-10,
58  -6, -4, -6, -7, -7, -3, -6, -1, -7, -1, -1,-17,
59  /*I*/ -5, -5, -5, -7, -6, -8, -5,-11, -9, 8, -1, -6, -1,
60  -2, -8, -7, -2,-14, -6, 2, -6, 5, -6, -1,-17,
61  /*L*/ -6, -8, -7,-12,-15, -5, -9,-10, -6, -1, 7, -8, 1,
62  -3, -7, -8, -7, -6, -7, -2, -9, 6, -7, -1,-17,
63  /*K*/ -7, 0, -1, -4,-14, -3, -4, -7, -6, -6, -8, 7, -2,
64  -14, -6, -4, -3,-12, -9, -9, -2, -7, -4, -1,-17,
65  /*M*/ -5, -4, -9,-11,-13, -4, -7, -8,-10, -1, 1, -2, 11,
66  -4, -8, -5, -4,-13,-11, -1,-10, 0, -5, -1,-17,
67  /*F*/ -8, -9, -9,-15,-13,-13,-14, -9, -6, -2, -3,-14, -4,
68  9,-10, -6, -9, -4, 2, -8,-10, -2,-13, -1,-17,
69  /*P*/ -2, -4, -6, -8, -8, -3, -5, -6, -4, -8, -7, -6, -8,
70  -10, 8, -2, -4,-14,-13, -6, -7, -7, -4, -1,-17,
71  /*S*/ 0, -3, 0, -4, -3, -5, -4, -2, -6, -7, -8, -4, -5,
72  -6, -2, 6, 0, -5, -7, -6, -1, -8, -5, -1,-17,
73  /*T*/ -1, -6, -2, -5, -8, -5, -6, -6, -7, -2, -7, -3, -4,
74  -9, -4, 0, 7,-13, -6, -3, -3, -5, -6, -1,-17,
75  /*W*/ -13, -2, -8,-15,-15,-13,-17,-15, -7,-14, -6,-12,-13,
76  -4,-14, -5,-13, 13, -5,-15,-10, -7,-14, -1,-17,
77  /*Y*/ -8,-10, -4,-11, -4,-12, -8,-14, -3, -6, -7, -9,-11,
78  2,-13, -7, -6, -5, 10, -7, -6, -7, -9, -1,-17,
79  /*V*/ -2, -8, -8, -8, -6, -7, -6, -5, -6, 2, -2, -9, -1,
80  -8, -6, -6, -3,-15, -7, 7, -8, 0, -6, -1,-17,
81  /*B*/ -3, -7, 6, 6,-12, -3, 1, -3, -1, -6, -9, -2,-10,
82  -10, -7, -1, -3,-10, -6, -8, 6, -8, 0, -1,-17,
83  /*J*/ -6, -7, -6,-10, -9, -5, -7,-10, -7, 5, 6, -7, 0,
84  -2, -7, -8, -5, -7, -7, 0, -8, 6, -6, -1,-17,
85  /*Z*/ -3, -4, -3, 1,-14, 6, 6, -5, -1, -6, -7, -4, -5,
86  -13, -4, -5, -6,-14, -9, -6, 0, -6, 6, -1,-17,
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,-17,
89  /***/ -17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,
90  -17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17, 1
91 };
93  "ARNDCQEGHILKMFPSTWYVBJZX*",
94  s_Pam30PSM,
95  -17
96 };
97 
int TNCBIScore
data types
Definition: raw_scoremat.h:45
const SNCBIPackedScoreMatrix NCBISM_Pam30
Definition: sm_pam30.c:92
static const TNCBIScore s_Pam30PSM[25 *25]
Entries for the PAM30 matrix at a scale of ln(2)/2.0.
Definition: sm_pam30.c:38
Modified on Tue Feb 27 05:50:20 2024 by modify_doxy.py rev. 669887