signal_seq.cpp

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/*  $Id: signal_seq.cpp 46773 2010-08-09 18:35:30Z dicuccio $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Authors:  Josh Cherry
 *
 * File Description:  Prediction of signal sequences from protein sequence
 *                    according to von Heijne, 1986 and 1987
 *
 */
 
 
#include <ncbi_pch.hpp>
#include <algo/sequence/signal_seq.hpp>
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
 
// Scoring matrix for eukaryotic signal sequences
// we have to declare these extern to be accessible from template on ForteCC.
extern const double const_EukMat[26][15];
extern const double const_BacMat[26][15];
 
const double const_EukMat[26][15] = {
    {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
    {0.0984401, -0.109199, -0.0350913, 0.0339016, 0.321584,
     0.216223, 0.216223, 0.159065, 0.544727, 0.0339016, 
     1.176, -0.882389, 1.70788, 0.216223, -0.882389}, // A
     {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // B (?)
    {-0.405465, 0.287682, 0.693147, 0.441833, 0.693147,
     1.13498, 0.287682, 0.575364, 0.105361, 0.287682,
     1.44036, -0.405465, 0.693147, 0.575364, -0.405465}, // C
    {-2.18605, -2.18605, -2.18605, -2.18605, -2.18605,
     -2.18605, -2.18605, -2.18605, -0.576613, -1.08744,
     -25.2119, -0.576613, -25.2119, 0.116534, 0.211844}, // D
    {-2.30259, -2.30259, -2.30259, -2.30259, -2.30259,
     -2.30259, -2.30259, -2.30259, -1.20397, -0.356675,
     -25.3284, -0.356675, -25.3284, 0.262364, 0.336472}, // E
    {0.842183, 0.474458, 0.675129, 0.675129, 0.0689929,
     0.223144, 1.16761, 0.842183, -0.336472, -0.113329,
     -24.7486, 0.842183, -24.7486, 0.0689929, -0.336472}, // F
    {-1.10691, -1.10691, -1.39459, -0.701446, -1.39459,
     0.0717439, -1.39459, -1.80006, 0.451234, 1.03316,
     -0.883768, -0.547295, 1.17036, -0.19062, -0.547295}, // G
    {-1.22378, -1.22378, -1.22378, -1.22378, -1.22378,
     -1.22378, -1.22378, -1.22378, 0.385662, -1.22378,
     -24.2496, 0.567984, -24.2496, 0.162519, -0.530628}, // H
    {0.70657, 0.70657, 0.0779615, -0.209721, 0.396415,
     -0.392042, -0.615186, 0.0779615, -0.392042, -2.00148,
     0.301105, -0.392042, -25.0273, 0.0779615, -0.0555699}, // I
    {-2.4248, -2.4248, -2.4248, -2.4248, -2.4248,
     -2.4248, -2.4248, -2.4248, -2.4248, -1.03851,
     -25.4507, -1.73166, -25.4507, -0.0269075, -0.227578}, // K
    {1.76947, 1.7263, 1.78346, 1.87624, 1.8635,
     1.31346, 1.66568, 1.39861, -0.19062, 0.642289,
     -0.413764, 0.502527, -2.49321, -0.413764, -1.10691}, // L
    {-0.993252, 0.105361, 0.952658, 0.393043, -0.993252,
     0.798508, -0.300105, -0.300105, -0.993252, -0.993252,
     -24.0191, -0.993252, -24.0191, -0.993252, -0.300105}, // M
    {-1.96009, -1.96009, -1.96009, -1.96009, -1.96009,
     -1.96009, -1.96009, -1.96009, -0.861482, -0.861482,
     -24.9859, 0.34249, -24.9859, -0.5738, -0.0141846}, // N
    {-1.30833, -2.00148, -1.30833, -2.00148, -2.00148,
     -0.615186, -2.00148, 0.0779615, 0.994252, 0.637577,
     -25.0273, -2.00148, -0.902868, -2.00148, 1.08956}, // P
    {-1.84055, -1.84055, -1.84055, -1.84055, -1.84055,
     -0.0487902, -1.84055, -1.84055, 0.462035, 0.238892,
     -24.8664, 1.04982, -0.741937, 1.10389, 0.462035}, // Q
    {-1.335, -2.02815, -2.02815, -2.02815, -2.02815,
     -2.02815, -2.02815, -2.02815, -0.0822381, -0.641854,
     -25.054, 0.679902, -25.054, 0.456758, 0.169076}, // R
    {-0.236389, -1.335, -0.354172, -0.641854, 0.131336,
     -0.131028, 0.274437, 0.338975, 0.824483, -0.0357181,
     0.701881, 0.3996, 0.562119, 0.274437, -0.131028}, // S
    {-1.57898, 0.0304592, -0.662688, -0.885832, -0.662688,
     0.292823, -0.326216, -0.326216, 0.212781, -0.480366,
     0.561087, -0.192684, -0.480366, -1.17351, 0.0304592}, // T
    {0.588787, 0.811931, 0.301105, 0.483427, 0.158004,
     0.301105, -0.00904984, 0.888892, -2.40695, 0.0779615,
     1.05879, -1.30833, -25.4328, -0.327504, 0.426268}, // V
    {0.798508, 0.510826, 0.510826, -0.587787, -0.587787,
     0.105361, 1.20397, 0.510826, -0.587787, 0.510826,
     -23.6136, 1.60944, -23.6136, 0.105361, -0.587787}, // W
    {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // X (?)
    {-1.72277, -1.72277, -0.336472, -1.72277, -1.72277,
     -1.72277, -0.624154, -1.72277, -1.72277, -1.02962,
     -24.7486, -0.113329, -24.7486, -1.72277, 0.223144}, // Y
    {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // Z (?)
    {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // U (?)
    {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0} // * (?)
};
 
 
// Scoring matrix for bacterial signal sequences
const double const_BacMat[26][15] = {
    {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
    {1.13943, 0.916291, 0.916291, 1.03407, 0.628609,
     0.782759, 0.446287, 0.628609, 0.782759, 0.782759,
     2.0149, -0.470004, 2.27084, 1.72722, 0.223144}, // A
    {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // B (?)
    {0, 0, 0, 0, 0,
     0, 0, 0, 0, 0,
     -23.0259, 0, -23.0259, 0, 0}, // C
    {-0.693147, -0.693147, -0.693147, -0.693147, -0.693147,
     -0.693147, -0.693147, -0.693147, -0.693147, -0.693147,
     -23.719, -0.693147, -23.719, 0, 1.38629}, // D
    {-0.788457, -0.788457, -0.788457, -0.788457, -0.788457,
     -0.788457, -0.788457, -0.788457, -0.788457, -0.788457,
     -23.8143, -0.788457, -23.8143, 0.597837, 1.29098}, // E
    {0.430783, 1.12393, 0.836248, 1.12393, -0.262364,
     -0.262364, 1.81708, -0.262364, 1.12393, -0.262364,
     -23.2882, 1.68355, -23.2882, -0.262364, -0.262364}, // F
    {0.393043, -0.300105, -0.300105, -0.300105, 0.105361,
     0.616186, -0.300105, 0.393043, -0.300105, -0.300105,
     -24.0191, -0.300105, -0.300105, -0.993252, -0.993252}, // G
    {0.223144, 0.223144, 0.223144, 0.223144, 0.223144,
     0.223144, 0.223144, 0.223144, 0.223144, 0.223144,
     -22.8027, 2.16905, -22.8027, 0.223144, 0.223144}, // H
    {0.567984, -0.530628, 1.07881, -0.530628, 1.07881,
     -0.530628, -0.530628, 0.567984, -0.530628, -0.530628,
     -23.5565, -0.530628, -23.5565, -0.530628, 0.162519}, // I
    {-0.916291, -0.916291, -0.916291, -0.916291, -0.916291,
     -0.916291, -0.916291, -0.916291, -0.916291, -0.916291,
     -23.9421, -0.223144, -23.9421, 0.182322, -0.916291}, // K
    {1.08619, 1.40464, 1.20397, 1.08619, 1.20397,
     1.5717, -0.993252, -0.993252, -0.300105, -0.300105,
     -0.993252, -0.300105, -24.0191, -0.993252, -0.993252}, // L
    {0.510826, 1.20397, 0.510826, 0.510826, 1.60944,
     1.20397, 1.60944, 0.510826, 0.510826, 1.20397,
     -22.515, 1.89712, -22.515, 0.510826, 0.510826}, // M
    {-0.470004, -0.470004, -0.470004, -0.470004, -0.470004,
     -0.470004, -0.470004, -0.470004, -0.470004, -0.470004,
     -23.4959, 0.628609, -23.4959, -0.470004, 0.916291}, // N
    {-0.530628, -0.530628, -0.530628, -0.530628, -0.530628,
     -0.530628, 0.162519, 0.567984, 1.07881, 0.162519,
     -23.5565, -0.530628, -23.5565, -0.530628, 1.07881}, // P
    {-0.336472, -0.336472, -0.336472, -0.336472, -0.336472,
     -0.336472, -0.336472, -0.336472, 0.356675, 0.356675,
     -23.3623, 0.76214, -23.3623, -0.336472, -0.336472}, // Q
    {-0.530628, -0.530628, -0.530628, -0.530628, -0.530628,
     -0.530628, -0.530628, -0.530628, -0.530628, -0.530628,
     -23.5565, -0.530628, -23.5565, -0.530628, -0.530628}, // R
    {-0.955511, -0.955511, -0.955511, 0.430783, 0.430783,
     -0.955511, 0.653926, 1.75254, 0.653926, 1.12393,
     0.653926, -0.262364, -0.262364, -0.955511, -0.955511}, // S
    {-0.0953102, -0.788457, 0.597837, -0.0953102, -0.0953102,
     -0.0953102, -0.0953102, -0.0953102, 0.820981, -0.788457,
     0.310155, -0.788457, -0.788457, -0.788457, -0.0953102}, // T
    {0.693147, 1.02962, -0.916291, 0.182322, -0.916291,
     0.470004, 1.02962, -0.916291, -0.916291, 0.470004,
     0.182322, -0.916291, -23.9421, -0.223144, -0.916291}, // V
    {0.916291, 0.916291, 0.916291, 0.916291, 0.916291,
     0.916291, 0.916291, 0.916291, 0.916291, 0.916291,
     -22.1096, 0.916291, -22.1096, 0.916291, 0.916291}, // W
    {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // X (?)
    {-0.262364, -0.262364, -0.262364, -0.262364, -0.262364,
     -0.262364, -0.262364, -0.262364, -0.262364, 0.836248,
     -23.2882, -0.262364, -23.2882, -0.262364, -0.262364}, // Y
    {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // Z (?)
    {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // U (?)
    {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}  // * (?)
};
 
 
template<class Seq>
void x_PredictSignalSeq(const Seq& seq, CSignalSeq::EDomain domain,
                        TSeqPos max_pos, TSeqPos& pos, double& score)
{
 
    if (seq.size() < 15) {
        throw runtime_error("Sequence length must be at least 15 "
                            "to predict signal sequence");
    }
    if (max_pos < 12) {
        throw runtime_error("max_pos must be at least 12 "
                            "to predict signal sequence");
    }
 
    const double (*Mat)[15];
    if (domain == CSignalSeq::eBacterial) {
        Mat = const_BacMat;
    } else {
        Mat = const_EukMat;
    }
 
    TSeqPos max_index = min((TSeqPos)seq.size() - 15, max_pos - 12);
    
    double max_score = -1e6;
    TSeqPos max_loc = 0;  // initialize to avoid compiler warning
    for (unsigned int i = 0;  i <= max_index;  i++) {
        double sum = 0;
        for (unsigned int j = 0;  j < 15;  j++) {
            int sub = (unsigned char)seq[i + j];
            sum += Mat[sub][j];
        }
        if (sum > max_score) {
            max_score = sum;
            max_loc = i;
        }
    }
    score = max_score;
    pos = max_loc + 12;  // position before cut
}
 
 
void CSignalSeq::Predict(const string& seq, EDomain domain,
                         TSeqPos max_pos, TSeqPos& pos, double& score)
{
    x_PredictSignalSeq(seq, domain, max_pos, pos, score);
}
 
 
void CSignalSeq::Predict(const vector<char>& seq, EDomain domain,
                         TSeqPos max_pos, TSeqPos& pos, double& score)
{
    x_PredictSignalSeq(seq, domain, max_pos, pos, score);
}
 
 
void CSignalSeq::Predict(const CSeqVector& seq, EDomain domain,
                         TSeqPos max_pos, TSeqPos& pos, double& score)
{
    string seq_ncbistdaa;
    CSeqVector vec(seq);
    vec.SetNcbiCoding();
    vec.GetSeqData(0, vec.size(), seq_ncbistdaa);
    x_PredictSignalSeq(seq_ncbistdaa, domain, max_pos, pos, score);
}
 
 
END_NCBI_SCOPE