1 /*==========================================================================
2 SeqAn - The Library for Sequence Analysis
4 ============================================================================
7 This library is free software; you can redistribute it and/or
8 modify it under the terms of the GNU Lesser General Public
9 License as published by the Free Software Foundation; either
10 version 3 of the License, or (at your option) any later version.
12 This library is distributed in the hope that it will be useful,
13 but WITHOUT ANY WARRANTY; without even the implied warranty of
14 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
15 Lesser General Public License for more details.
17 ============================================================================
18 $Id: shape_predefined.h,v 1.1 2008/08/25 16:20:05 langmead Exp $
19 ==========================================================================*/
21 #ifndef SEQAN_HEADER_SHAPE_PREDEFINED_H
22 #define SEQAN_HEADER_SHAPE_PREDEFINED_H
24 //SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
26 namespace SEQAN_NAMESPACE_MAIN
29 //////////////////////////////////////////////////////////////////////////////
30 // some predefined gapped shapes
33 //////////////////////////////////////////////////////////////////////////////
35 // B.Ma and J.Tromp and M.Li,
36 // "PatternHunter: faster and more sensitive homology search"
37 // Bioinformatics 18, 2002
45 typedef FixedGappedShape<
46 HardwiredShape< 1, 1, 2, 3, 2, 3, 1, 2, 1, 1 >
51 //////////////////////////////////////////////////////////////////////////////
53 // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
65 // 65% 0.747975 70% 0.897741
66 // 75% 0.973134 80% 0.996226
68 typedef FixedGappedShape<
69 HardwiredShape< 1, 1, 2, 2, 3, 3, 1, 1 >
72 typedef FixedGappedShape<
73 HardwiredShape< 1, 2, 3, 1, 3, 1, 1, 2 >
76 typedef FixedGappedShape<
77 HardwiredShape< 1, 1, 2, 4, 2, 1, 2, 1 >
82 //////////////////////////////////////////////////////////////////////////////
84 // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
93 // 11100010010000101011
96 // 65% 0.767413 70% 0.910949
97 // 75% 0.978558 80% 0.997357
99 typedef FixedGappedShape<
100 HardwiredShape< 1, 1, 2, 1, 2, 3, 1, 1 >
101 > ShapeIlie_9_1323_1;
103 typedef FixedGappedShape<
104 HardwiredShape< 1, 2, 5, 1, 3, 2, 1, 1 >
105 > ShapeIlie_9_1323_2;
107 typedef FixedGappedShape<
108 HardwiredShape< 1, 1, 4, 3, 5, 2, 2, 1 >
109 > ShapeIlie_9_1323_3;