| Class HardwiredShape A structure to define a fixed gapped shape. HardwiredShape<P1, P2, ..., Pn> Parameters
P1, P2, |
Remarks You can use this structure to define your one gapped shapes in conjunction with GappedShape. Note: The shape 1100101 corresponds to HardwiredShape<1,3,2>. Note: The following predefined shapes are already available in seqan/index/shape_predefined.h: File "shape_predefined.h"
1 | /*==========================================================================
2 | SeqAn - The Library for Sequence Analysis
3 | http://www.seqan.de
4 | ============================================================================
5 | Copyright (C) 2007
6 |
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.
11 |
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.
16 |
17 | ============================================================================
18 | $Id: shape_predefined.h 3341 2009-02-02 14:58:46Z doering@PCPOOL.MI.FU-BERLIN.DE $
19 | ==========================================================================*/
20 |
21 | #ifndef SEQAN_HEADER_SHAPE_PREDEFINED_H
22 | #define SEQAN_HEADER_SHAPE_PREDEFINED_H
23 |
24 | //SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
25 |
26 | namespace SEQAN_NAMESPACE_MAIN
27 | {
28 |
29 | //////////////////////////////////////////////////////////////////////////////
30 | // some predefined gapped shapes
31 |
32 |
33 | //////////////////////////////////////////////////////////////////////////////
34 | // Single seed of
35 | // B.Ma and J.Tromp and M.Li,
36 | // "PatternHunter: faster and more sensitive homology search"
37 | // Bioinformatics 18, 2002
38 | //
39 | // weight:11
40 | // length:18
41 | //
42 | // shape:
43 | // 111010010100110111
44 |
45 | typedef GappedShape<
46 | HardwiredShape< 1, 1, 2, 3, 2, 3, 1, 2, 1, 1 >
47 | > ShapePatternHunter;
48 |
49 |
50 |
51 | //////////////////////////////////////////////////////////////////////////////
52 | // Multiple seeds of
53 | // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
54 | // WABI, 2007
55 | //
56 | // weight:9
57 | // length:15
58 | //
59 | // shapes:
60 | // 111010100100111
61 | // 110100110011101
62 | // 111010001011011
63 | //
64 | // sensitivity:
65 | // 65% 0.747975 70% 0.897741
66 | // 75% 0.973134 80% 0.996226
67 |
68 | typedef GappedShape<
69 | HardwiredShape< 1, 1, 2, 2, 3, 3, 1, 1 >
70 | > ShapeIlie_9_15_1;
71 |
72 | typedef GappedShape<
73 | HardwiredShape< 1, 2, 3, 1, 3, 1, 1, 2 >
74 | > ShapeIlie_9_15_2;
75 |
76 | typedef GappedShape<
77 | HardwiredShape< 1, 1, 2, 4, 2, 1, 2, 1 >
78 | > ShapeIlie_9_15_3;
79 |
80 |
81 |
82 | //////////////////////////////////////////////////////////////////////////////
83 | // Multiple seeds of
84 | // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
85 | // WABI 2007
86 | //
87 | // weight:9
88 | // length:13..23
89 | //
90 | // shapes:
91 | // 1110110100111
92 | // 11010000110010111
93 | // 11100010010000101011
94 | //
95 | // sensitivity:
96 | // 65% 0.767413 70% 0.910949
97 | // 75% 0.978558 80% 0.997357
98 |
99 | typedef GappedShape<
100 | HardwiredShape< 1, 1, 2, 1, 2, 3, 1, 1 >
101 | > ShapeIlie_9_1323_1;
102 |
103 | typedef GappedShape<
104 | HardwiredShape< 1, 2, 5, 1, 3, 2, 1, 1 >
105 | > ShapeIlie_9_1323_2;
106 |
107 | typedef GappedShape<
108 | HardwiredShape< 1, 1, 4, 3, 5, 2, 2, 1 >
109 | > ShapeIlie_9_1323_3;
110 |
111 |
112 | } // namespace seqan
113 |
114 | #endif
See Also GappedShape, Shape SeqAn - Sequence Analysis Library - www.seqan.de