seqan3::align_cfg::method_global Class Reference

Sets the global alignment method. More...

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

Inheritance diagram for seqan3::align_cfg::method_global:

Public Member Functions
Constructors, destructor and assignment
	method_global ()=default
	Defaulted.
	method_global (method_global const &)=default
	Defaulted.
	method_global (method_global &&)=default
	Defaulted.
method_global &	operator= (method_global const &)=default
	Defaulted.
method_global &	operator= (method_global &&)=default
	Defaulted.
	~method_global ()=default
	Defaulted.
constexpr	method_global (seqan3::align_cfg::free_end_gaps_sequence1_leading free_sequence1_leading, seqan3::align_cfg::free_end_gaps_sequence2_leading free_sequence2_leading, seqan3::align_cfg::free_end_gaps_sequence1_trailing free_sequence1_trailing, seqan3::align_cfg::free_end_gaps_sequence2_trailing free_sequence2_trailing) noexcept
	Construct method_global with a specific free end gap configuration.

Public Attributes
bool	free_end_gaps_sequence1_leading {false}
	If set to true, leading gaps in sequence1 are not penalised when computing the optimal alignment.
bool	free_end_gaps_sequence1_trailing {false}
	If set to true, trailing gaps in sequence1 are not penalised when computing the optimal alignment.
bool	free_end_gaps_sequence2_leading {false}
	If set to true, leading gaps in sequence2 are not penalised when computing the optimal alignment.
bool	free_end_gaps_sequence2_trailing {false}
	If set to true, trailing gaps in sequence2 are not penalised when computing the optimal alignment.

Detailed Description

Sets the global 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.

Global Alignment:

--T--CC-C-AGT--TATGT-CAGGGGACACG-A-GCATGCAGA-GAC
  |  || |  ||  | | | |||    || | | |  | ||||   |
AATTGCCGCC-GTCGT-T-TTCAG----CA-GTTATG-T-CAGAT--C

Finding the optimal global alignment of two sequences is solved by the Needleman-Wunsch algorithm.
Semi-global Alignment (e.g. overlapping sequences):

                  TCCCAGTTATGTCAGgggacacgagcatgcagagac
                  |||||||||||||||
aattgccgccgtcgttttTCCCAGTTATGTCAG

The semi-global alignment is a specially configured global alignment, namely we do not penalize gaps at the ends of the alignment. Semi-global alignments are often used in genome assembly applications when trying to find matching overlaps.

Example

// 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
 
#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 global alignment for DNA sequences
    auto min_cfg = seqan3::align_cfg::method_global{}
                 | seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
                                                                                       seqan3::mismatch_score{-5}}}
                 | seqan3::align_cfg::gap_cost_affine{seqan3::align_cfg::open_score{-10},
                                                      seqan3::align_cfg::extension_score{-1}};
 
    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.

Constructor & Destructor Documentation

method_global()

constexpr seqan3::align_cfg::method_global::method_global ( seqan3::align_cfg::free_end_gaps_sequence1_leading  free_sequence1_leading, seqan3::align_cfg::free_end_gaps_sequence2_leading  free_sequence2_leading, seqan3::align_cfg::free_end_gaps_sequence1_trailing  free_sequence1_trailing, seqan3::align_cfg::free_end_gaps_sequence2_trailing  free_sequence2_trailing  )

inlineconstexprnoexcept

Construct method_global with a specific free end gap configuration.

Parameters

[in]	free_sequence1_leading	An instance of seqan3::align_cfg::free_end_gaps_sequence1_leading that indicates whether leading gaps in sequence1 should be free (not penalised).
[in]	free_sequence2_leading	An instance of seqan3::align_cfg::free_end_gaps_sequence2_leading that indicates whether leading gaps in sequence2 should be free (not penalised).
[in]	free_sequence1_trailing	An instance of seqan3::align_cfg::free_end_gaps_sequence1_trailing that indicates whether trailing gaps in sequence1 should be free (not penalised).
[in]	free_sequence2_trailing	An instance of seqan3::align_cfg::free_end_gaps_sequence2_trailing that indicates whether trailing gaps in sequence2 should be free (not penalised).

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

• align_config_method.hpp