SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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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
 method_local (method_local const &)=default
 method_local (method_local &&)=default
method_localoperator= (method_local const &)=default
method_localoperator= (method_local &&)=default
 ~method_local ()=default

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):


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.


// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
using namespace seqan3::literals;
int main()
// configure a local alignment for DNA sequences
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
Provides global and local alignment configurations.
Provides seqan3::align_cfg::scoring_scheme.
Provides pairwise alignment function.
Sets the local alignment method.
Definition align_config_method.hpp:42
Sets the scoring scheme for the alignment algorithm.
Definition align_config_scoring_scheme.hpp:42
A data structure for managing and computing the score of two nucleotides.
Definition nucleotide_scoring_scheme.hpp:35
Provides seqan3::debug_stream and related types.
Provides seqan3::dna4, container aliases and string literals.
constexpr auto align_pairwise(sequence_t &&seq, alignment_config_t const &config)
Computes the pairwise alignment for a pair of sequences or a range over sequence pairs.
Definition align_pairwise.hpp:131
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition debug_stream.hpp:37
The SeqAn namespace for literals.
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
SeqAn specific customisations in the standard namespace.
Provides seqan3::nucleotide_scoring_scheme.
A strong type of underlying type score_type that represents the score of two matching characters.
Definition scoring_scheme_base.hpp:38
A strong type of underlying type score_type that represents the score two different characters.
Definition scoring_scheme_base.hpp:63
T tie(T... args)
For a complete overview, take a look at Pairwise Alignments.

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