| 1 | // ==========================================================================
|
| 2 | // SeqAn - The Library for Sequence Analysis
|
| 3 | // ==========================================================================
|
| 4 | // Copyright (c) 2006-2013, Knut Reinert, FU Berlin
|
| 5 | // All rights reserved.
|
| 6 | //
|
| 7 | // Redistribution and use in source and binary forms, with or without
|
| 8 | // modification, are permitted provided that the following conditions are met:
|
| 9 | //
|
| 10 | // * Redistributions of source code must retain the above copyright
|
| 11 | // notice, this list of conditions and the following disclaimer.
|
| 12 | // * Redistributions in binary form must reproduce the above copyright
|
| 13 | // notice, this list of conditions and the following disclaimer in the
|
| 14 | // documentation and/or other materials provided with the distribution.
|
| 15 | // * Neither the name of Knut Reinert or the FU Berlin nor the names of
|
| 16 | // its contributors may be used to endorse or promote products derived
|
| 17 | // from this software without specific prior written permission.
|
| 18 | //
|
| 19 | // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
| 20 | // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
| 21 | // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
| 22 | // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
|
| 23 | // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
| 24 | // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
| 25 | // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
| 26 | // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
|
| 27 | // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
|
| 28 | // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
|
| 29 | // DAMAGE.
|
| 30 | //
|
| 31 | // ==========================================================================
|
| 32 | // Author: David Weese <david.weese@fu-berlin.de>
|
| 33 | // ==========================================================================
|
| 34 |
|
| 35 | #ifndef SEQAN_HEADER_SHAPE_PREDEFINED_H
|
| 36 | #define SEQAN_HEADER_SHAPE_PREDEFINED_H
|
| 37 |
|
| 38 | //SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file
|
| 39 |
|
| 40 | namespace SEQAN_NAMESPACE_MAIN
|
| 41 | {
|
| 42 |
|
| 43 | //////////////////////////////////////////////////////////////////////////////
|
| 44 | // some predefined gapped shapes
|
| 45 |
|
| 46 |
|
| 47 | //////////////////////////////////////////////////////////////////////////////
|
| 48 | // Single seed of
|
| 49 | // B.Ma and J.Tromp and M.Li,
|
| 50 | // "PatternHunter: faster and more sensitive homology search"
|
| 51 | // Bioinformatics 18, 2002
|
| 52 | //
|
| 53 | // weight:11
|
| 54 | // length:18
|
| 55 | //
|
| 56 | // shape:
|
| 57 | // 111010010100110111
|
| 58 |
|
| 59 | typedef GappedShape<
|
| 60 | HardwiredShape< 1, 1, 2, 3, 2, 3, 1, 2, 1, 1 >
|
| 61 | > ShapePatternHunter;
|
| 62 |
|
| 63 |
|
| 64 |
|
| 65 | //////////////////////////////////////////////////////////////////////////////
|
| 66 | // Multiple seeds of
|
| 67 | // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
|
| 68 | // WABI, 2007
|
| 69 | //
|
| 70 | // weight:9
|
| 71 | // length:15
|
| 72 | //
|
| 73 | // shapes:
|
| 74 | // 111010100100111
|
| 75 | // 110100110011101
|
| 76 | // 111010001011011
|
| 77 | //
|
| 78 | // sensitivity:
|
| 79 | // 65% 0.747975 70% 0.897741
|
| 80 | // 75% 0.973134 80% 0.996226
|
| 81 |
|
| 82 | typedef GappedShape<
|
| 83 | HardwiredShape< 1, 1, 2, 2, 3, 3, 1, 1 >
|
| 84 | > ShapeIlieA1;
|
| 85 |
|
| 86 | typedef GappedShape<
|
| 87 | HardwiredShape< 1, 2, 3, 1, 3, 1, 1, 2 >
|
| 88 | > ShapeIlieA2;
|
| 89 |
|
| 90 | typedef GappedShape<
|
| 91 | HardwiredShape< 1, 1, 2, 4, 2, 1, 2, 1 >
|
| 92 | > ShapeIlieA3;
|
| 93 |
|
| 94 |
|
| 95 |
|
| 96 | //////////////////////////////////////////////////////////////////////////////
|
| 97 | // Multiple seeds of
|
| 98 | // L.Ilie and S.Ilie, "Fast Computation of Good Multiple Spaced Seeds"
|
| 99 | // WABI 2007
|
| 100 | //
|
| 101 | // weight:9
|
| 102 | // length:13..23
|
| 103 | //
|
| 104 | // shapes:
|
| 105 | // 1110110100111
|
| 106 | // 11010000110010111
|
| 107 | // 11100010010000101011
|
| 108 | //
|
| 109 | // sensitivity:
|
| 110 | // 65% 0.767413 70% 0.910949
|
| 111 | // 75% 0.978558 80% 0.997357
|
| 112 |
|
| 113 | typedef GappedShape<
|
| 114 | HardwiredShape< 1, 1, 2, 1, 2, 3, 1, 1 >
|
| 115 | > ShapeIlieB1;
|
| 116 |
|
| 117 | typedef GappedShape<
|
| 118 | HardwiredShape< 1, 2, 5, 1, 3, 2, 1, 1 >
|
| 119 | > ShapeIlieB2;
|
| 120 |
|
| 121 | typedef GappedShape<
|
| 122 | HardwiredShape< 1, 1, 4, 3, 5, 2, 2, 1 >
|
| 123 | > ShapeIlieB3;
|
| 124 |
|
| 125 |
|
| 126 | } // namespace seqan
|
| 127 |
|
| 128 | #endif
|