Function
globalAlignmentScore
Computes the best global pairwise alignment score.
Parameters
Horizontal gapped sequence in alignment matrix. Types: String | |
Vertical gapped sequence in alignment matrix. Types: String | |
A StringSet containing two sequences. Types: StringSet | |
The scoring scheme to use for the alignment.
Note that the user is responsible for ensuring that the scoring scheme is compatible with Types: Score | |
The AlignConfig to use for the alignment. Types: AlignConfig | |
Optional lower diagonal. Types: | |
Optional upper diagonal. Types: | |
The Tag for picking the alignment algorithm. |
Remarks
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.
Return Values
SeqAn - Sequence Analysis Library - www.seqan.de