fn() globalAlignmentScore
Computes the best global pairwise alignment score.

Defined in <seqan/align.h>
Signature TScoreVal globalAlignmentScore(seqH, seqV, scoringScheme[, alignConfig][, lowerDiag, upperDiag][, algorithmTag]); TScoreVal globalAlignmentScore(strings, scoringScheme[, alignConfig][, lowerDiag, upperDiag][, algorithmTag]); TScoreVal globalAlignmentScore(seqH, seqV, {MyersBitVector | MyersHirschberg}); TScoreVal globalAlignmentScore(strings, {MyersBitVector | MyersHirschberg});

Parameters

seqH Horizontal gapped sequence in alignment matrix. Types: String
seqV Vertical gapped sequence in alignment matrix. Types: String
strings A StringSet containing two sequences. Type: StringSet.
alignConfig The AlignConfig to use for the alignment. Type: AlignConfig
scoringScheme The scoring scheme to use for the alignment. Note that the user is responsible for ensuring that the scoring scheme is compatible with algorithmTag. Type: Score.
lowerDiag Optional lower diagonal. Types: int
upperDiag Optional upper diagonal. Types: int
algorithmTag The Tag for picking the alignment algorithm. Types: PairwiseLocalAlignmentAlgorithms.

Return Values

TScoreVal Score value of the resulting alignment (Metafunction: Value of the type of scoringScheme).

Detailed Description

This function does not perform the (linear time) traceback step after the (mostly quadratic time) dynamic programming step. Note that Myers' bit-vector algorithm does not compute an alignment (only in the Myers-Hirschberg variant) but scores can be computed using globalAlignmentScore.

The same limitations to algorithms as in globalAlignment apply. Furthermore, the MyersBitVector and MyersHirschberg variants can only be used without any other parameter.

Data Races

Thread safety unknown!

See Also