Interfaces
Table of Contents
Interfaces
- MoleculeAwareScoringInterface
- Interface MoleculeAwareScoringInterface - implemented by a scoring that only means something for
some molecules (PAM250 for proteins, the IUPAC nucleotide scoring for DNA and RNA). The aligners
refuse a sequence it does not support, instead of scoring A, C, G and T as alanine, cysteine,
glycine and threonine. A scoring that does not implement it is taken to suit any molecule. Kept
apart from SubstitutionScoringInterface, so that interface keeps its single method.
- NeedlemanWunschAlignerInterface
- Interface NeedlemanWunschAlignerInterface - computes the optimal end-to-end (global) alignment of
two sequences under a linear gap penalty.
- SemiGlobalAlignerInterface
- Interface SemiGlobalAlignerInterface - aligns two sequences without penalizing gaps at either end
of either sequence, so a short sequence fully contained in a longer one (a primer inside a vector,
an overlap between two fragments to assemble) scores as if the longer sequence's untouched flanks
were never there.
- SmithWatermanAlignerInterface
- Interface SmithWatermanAlignerInterface - finds the highest-scoring locally similar subsequence of
two sequences under a linear gap penalty, rather than aligning them end to end.
- SubstitutionScoringInterface
- Interface SubstitutionScoringInterface - lets a pairwise aligner stay ignorant of how two symbols
are scored against each other, whether by a flat match/mismatch rule or a substitution matrix such
as PAM250.