1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
|
// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <seqan3/alignment/pairwise/all.hpp> // for seqan3::align_cfg and seqan3::align_pairwise
#include <seqan3/alignment/scoring/all.hpp> // for seqan3::aminoacid_scoring_scheme and
// seqan3::aminoacid_similarity_matrix
#include <seqan3/alphabet/aminoacid/aa27.hpp> // for seqan3::operator""_aa27
#include <seqan3/core/debug_stream.hpp>
int main()
{
using namespace seqan3::literals;
auto seq1 = "QFSEEILSDIYCWMLQCGQERAV"_aa27;
auto seq2 = "AFLPGWQEENKLSKIWMKDCGCLW"_aa27;
// Configure the alignment kernel.
auto config =
seqan3::align_cfg::method_global{}
| seqan3::align_cfg::scoring_scheme{seqan3::aminoacid_scoring_scheme{
seqan3::aminoacid_similarity_matrix::blosum62}}
| seqan3::align_cfg::gap_cost_affine{seqan3::align_cfg::open_score{-9}, seqan3::align_cfg::extension_score{-2}};
for (auto const & res : seqan3::align_pairwise(std::tie(seq1, seq2), config))
seqan3::debug_stream << "Score: " << res.score() << '\n';
}
|
