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

DefaultFindBeginPatternSpec | Type of the default findBegin pattern specialization, given a score. (Score)
SequenceEntryForScore | Returns representation type for a character of a position in a sequence. (Score)
Value | Type of the items in the container or behind an iterator. (Score)

Member Functions

Score | Constructor (Score)

Functions

alignmentEvaluation | Given a multiple alignment, this function calculates all kinds of alignment statistics. (Score)
bandedChainAlignment | Computes the best global pairwise alignment between two sequences given a non-empty seed chain. (Score)
buildAlignmentGraph | Builds an Alignment Graph from a set of input alignments. (Score)
globalAlignment | Computes the best global pairwise alignment. (Score)
globalAlignmentScore | Computes the best global pairwise alignment score. (Score)
globalMsaAlignment | Computes a global multiple alignment. (Score)
loadScoreMatrix | Load a score matrix from a file.
localAlignment | Computes the best pairwise local alignment using the Smith-Waterman algorithm. (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)
score | Returns the score for aligning the entries entryH and entryV. (Score)
scoreGap | Score for gaps. (Score)
scoreGapExtend | Score for extending gaps. (Score)
scoreGapExtendHorizontal | Returns the score for extending a gap in horizontal direction. (Score)
scoreGapExtendVertical | Returns the score for extending a gap in vertical direction. (Score)
scoreGapHorizontal | Returns the score for a gap in horizontal direction. (Score)
scoreGapOpen | Score for opening a gap. (Score)
scoreGapOpenHorizontal | Returns the score for opening a gap in horizontal direction. (Score)
scoreGapOpenVertical | Returns the score for opening a gap in vertical direction. (Score)
scoreGapVertical | Returns the score for a gap in vertical direction. (Score)
scoreMatch | Match score. (Score)
scoreMismatch | Mismatch score. (Score)
sequenceEntryForScore | Helper function for element access, depending on score type. (Score)
setDefaultScoreMatrix | Set the value of the given matrix to the default value.
setScore | Set the substitution score between two values.
setScoreGap | Set gap opening and extension score. (Score)
setScoreGapExtend | Set gap extension score. (Score)
setScoreGapOpen | Set gap opening score. (Score)
setScoreMatch | Set match score. (Score)
setScoreMismatch | Set mismatch score. (Score)
splitAlignment | Compute split alignments. (Score)
sumOfPairsScore | Given a multiple alignment, this function calculates the sum-of-pairs score. (Score)
write | Write a score matrix to a stream.

Shortcuts

Blosum30 | Blosum30 scoring matrix.
Blosum45 | Blosum45 scoring matrix.
Blosum62 | Blosum62 scoring matrix.
Blosum80 | Blosum80 scoring matrix.
Pam120 | Pam120 scoring matrix.
Pam200 | Pam200 scoring matrix.
Pam250 | Pam250 scoring matrix.
Pam40 | Pam40 scoring matrix.
Vtml200 | Vtml200 scoring matrix.

Example Programs
Local Alignments, Global Alignments
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2014/10/13 16:13:00