localAlignment

Function

localAlignment

Computes the best local alignment of two sequences.

localAlignment(align, score, tag)

localAlignment(align, score)

localAlignment(align, sw_finder, score, cutoff, tag)

localAlignment(align, sw_finder, score, cutoff, diagLow, diagHigh, tag)

localAlignment(strSet, score, tag)
localAlignment(graph, score, tag)
localAlignment(file, strSet, score, tag)

Include Headers

seqan/graph_align.h

Parameters

align	Alignment object to use. Types: Align
cutoff	Alignments with scores < cutoff will be discarded.
diagLow	The lowest diagonal of the alignment matrix that will be computed for banded alignment.
diagHigh	The highest diagonal of the alignment matrix that will be computed for banded alignment.
tag	A tag indicating the alignment algorithm to use Types: BandedWatermanEggert, SmithWaterman, WatermanEggert Remarks: SmithWaterman
strSet	A string set with 2 sequences. Types: StringSet Remarks: If an alignment graph is used that graph must contain a string set with two sequences
graph	The alignment graph having 2 sequences. Types: Alignment Graph
file	A file stream or std::cout to write a textual alignment
score	The score values to be used for computing the alignment. Types: Score

Return Values

The maximum score of the best local alignment.

Example Programs