seqan3::align_cfg::method_local Class Reference

Sets the local alignment method. More...

#include <seqan3/alignment/configuration/align_config_method.hpp>

Inheritance diagram for seqan3::align_cfg::method_local:

Public Member Functions
Constructors, destructor and assignment
	method_local ()=default
	Defaulted.
	method_local (method_local const &)=default
	Defaulted.
	method_local (method_local &&)=default
	Defaulted.
method_local &	operator= (method_local const &)=default
	Defaulted.
method_local &	operator= (method_local &&)=default
	Defaulted.
	~method_local ()=default
	Defaulted.

Detailed Description

Sets the local alignment method.

There are several methods for sequence alignment. We distinguish between local and global alignments. The semi-global alignment is implemented as a variation of the global alignment.

Local Alignment (better suited to find conserved segments):

                  tccCAGTTATGTCAGgggacacgagcatgcagagac
                     ||||||||||||
aattgccgccgtcgttttcagCAGTTATGTCAGatc

A local alignment is effectively a global alignment of two partial sequences. For example when two genes from different species are similar in short conserved regions and dissimilar in the remaining regions. A global alignment would not find the local matching because it would try to align the entire sequence. This is solved by the Smith-Waterman algorithm.

Example

// 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/configuration/align_config_method.hpp>
#include <seqan3/alignment/configuration/align_config_scoring_scheme.hpp>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
 
using namespace seqan3::literals;
 
int main()
{
    // configure a local alignment for DNA sequences
    auto min_cfg = seqan3::align_cfg::method_local{}
                 | seqan3::align_cfg::scoring_scheme{
                     seqan3::nucleotide_scoring_scheme{seqan3::match_score{4}, seqan3::mismatch_score{-5}}};
 
    auto seq1 = "TCGT"_dna4;
    auto seq2 = "ACGA"_dna4;
    for (auto res : seqan3::align_pairwise(std::tie(seq1, seq2), min_cfg))
        seqan3::debug_stream << res.score() << '\n'; // print out the alignment score
}

Remarks

For a complete overview, take a look at Pairwise Alignments.

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The documentation for this class was generated from the following file:

• align_config_method.hpp