Score

Class

Score

A scoring scheme.

Score


EditDistance	Score Matrix	Simple Score

Score<TValue, TSpec>

Include Headers

seqan/score.h

Parameters

TValue	The value type. Default: int
TSpec	The specializing type. Default: Tag.Simple

Specializations

EditDistance	Edit distance scoring scheme.
Score Matrix	A general scoring matrix.
Simple Score	Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps.

Metafunctions

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

Member Functions

Score

Constructor

Functions

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

Examples

1	Score<int> scoreScheme(5, -6, -2, -11); // Initialize Score object with affine gap costs.
2	int score = globalAlignment(align, scoreScheme); // Computes a global alignment usign the defined scoring scheme.
3
4	std::cout << "Score = " << score << std::endl;
5	std::cout << "Alignment:" << std::endl;
6	std::cout << align << std::endl;

Snippet from "score.cpp"

The output is as follows:

Score = 66
Alignment:
0     .    :    .    :    .
  ACGTG--GATCGGTGACTTACGGACTG
  |||||  ||   |||| ||||||||||
  ACGTGTTGA---GTGA-TTACGGACTG

Example Programs

Local Alignments, Global Alignments

SeqAn - Sequence Analysis Library - www.seqan.de