Score Matrix

Class Specialization

Score Matrix

A general scoring matrix.

Score Matrix

Score<TValue, ScoreMatrix<TSequenceValue, TSpec> >

Include Headers

seqan/score.h

Parameters

TValue	Type of the score values. Default: int
TSequenceValue	Type of alphabet underlying the matrix. Default: AminoAcid

Specialization of

Metafunctions

DefaultFindBeginPatternSpec	Type of the default findBegin pattern specialization, given a score. (Score)
Value	Type of the items in the container. (Score)

Member Functions

Score	Constructor.
Score	Constructor (Score)

Functions

alignmentEvaluation	Given a multiple alignment, this function calculates all kinds of alignment statistics. (Score)
globalAlignment	Computes the best global alignment of the two sequences. (Score)
globalMsaAlignment	Computes a global multiple alignment. (Score)
loadScoreMatrix	Load a score matrix from a file.
localAlignment	Computes the best local alignment of two sequences. (Score)
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. (Score)
multiLocalAlignment	Computes multiple local alignments of two sequences. (Score)
score	Returns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme. (Score)
score	Returns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme. (Score)
setDefaultScoreMatrix	Set the value of the given matrix to the default value.
setScore	Set the substitution score between two values.
sumOfPairsScore	Given a multiple alignment, this function calculates the sum-of-pairs score. (Score)

Shortcuts

Example Programs

SeqAn - Sequence Analysis Library - www.seqan.de