Align

Class

Align

An alignment of sequences.

Align<TSource, TSpec>

Include Headers

seqan/align.h

Parameters

TSource	Type of the ungapped sequences. Metafunctions: Source
TSpec	The specializing type. Metafunctions: Spec Default: ArrayGaps

Remarks

The default implementation of Align stores the alignment in a set of Gaps<TSource,TSpec> objects. Hence, the default implementation is row-based, so it will be faster to access the alignment row-wise than column-wise.

Metafunctions

Col	Type of a column in an alignment.
Cols	Type of column container of an alignment.
GetValue	Type for reading values.
Reference	Reference type.
Row	Type of a row in an alignment.
Rows	Type of row container of an alignment.
Source	Return underlying sequence of Gaps/Alignments.
StringSetType	Return type of stringSet function.
Value	Type of the items in the container or behind an iterator.

Functions

bamRecordToAlignment	Convert BamAlignmentRecord to an Align object.
bandedChainAlignment	Computes the best global pairwise alignment between two sequences given a non-empty seed chain.
col	A column in an alignment.
cols	The container of columns in an alignment.
detach	Makes an object independent from other objects.
globalAlignment	Computes the best global pairwise alignment.
integrateAlign	Integrates an alignment into another by copying the gaps.
localAlignment	Computes the best pairwise local alignment using the Smith-Waterman algorithm.
matchRefinement	Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping.
nextLocalAlignment	Compute next suboptimal local alignment.
row	A row in an alignment.
rows	The container of rows in an alignment.
setStrings	Loads the sequences of a stringset into an alignment.
splitAlignment	Compute split alignments.
stringSet	Gets the string set of an alignment graph.

Examples

File "align.cpp"

1	#include <seqan/basic.h>
2	#include <seqan/sequence.h>
3	#include <seqan/file.h> // for I/O
4	#include <seqan/align.h>
5	#include <seqan/score.h>
6
7	using namespace seqan;
8
9	int main()
10	{
11	StringSet<DnaString> stringSet;
12	appendValue(stringSet, "AGTTTAATCA");
13	appendValue(stringSet, "AGTATACGA");
14
15	Align<DnaString> align(stringSet); // Initialize the Align object using a StringSet.
16
17	int score = globalAlignment(align, EditDistanceScore()); // Compute a global alingment using the Align object.
18
19	std::cout << "score = " << score << std::endl;
20	std::cout << "align\n" << align << std::endl;
21
22	return 0;
23	}

The output is as follows:

score = -4
align
  0     .    :
    AGTTTAATCA
    ||| | |  |
    AGTAT-ACGA

Example Programs

Local Alignments, Global Alignments