Class Specialization
Score Matrix
A general scoring matrix.
Score
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
Score
Metafunctions
DefaultFindBeginPatternSpecType of the default findBegin pattern specialization, given a score. (Score)
ValueType of the items in the container or behind an iterator. (Score)
Member Functions
ScoreConstructor (Score)
Functions
alignmentEvaluationGiven a multiple alignment, this function calculates all kinds of alignment statistics. (Score)
buildAlignmentGraphBuilds an Alignment Graph from a set of input alignments. (Score)
globalAlignmentComputes the best global pairwise alignment. (Score)
globalAlignmentScoreComputes the best global pairwise alignment score. (Score)
globalMsaAlignmentComputes a global multiple alignment. (Score)
loadScoreMatrixLoad a score matrix from a file.
localAlignmentComputes the best pairwise local alignment using the Smith-Waterman algorithm. (Score)
matchRefinementRefines (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)
scoreReturns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme. (Score)
scoreGapScore for gaps. (Score)
scoreGapExtendScore for extending gaps. (Score)
scoreGapOpenScore for opening a gap. (Score)
scoreMatchMatch score. (Score)
scoreMismatchMismatch score. (Score)
setDefaultScoreMatrixSet the value of the given matrix to the default value.
setScoreSet the substitution score between two values.
setScoreGapSet gap opening and extension score. (Score)
setScoreGapExtendSet gap extension score. (Score)
setScoreGapOpenSet gap opening score. (Score)
setScoreMatchSet match score. (Score)
setScoreMismatchSet mismatch score. (Score)
sumOfPairsScoreGiven a multiple alignment, this function calculates the sum-of-pairs score. (Score)
write 
Shortcuts
Blosum30Blosum30 scoring matrix.
Blosum45Blosum45 scoring matrix.
Blosum62Blosum62 scoring matrix.
Blosum80Blosum80 scoring matrix.
Pam120Pam120 scoring matrix.
Pam200Pam200 scoring matrix.
Pam250Pam250 scoring matrix.
Pam40Pam40 scoring matrix.
Vtml200Vtml200 scoring matrix.
SeqAn - Sequence Analysis Library - www.seqan.de
 

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