salign-methods {crosshybDetector} | R Documentation |
Computes optimal pairwise alignment of 2 protein sequences.
obj1 |
see above |
obj2 |
see above |
sub |
Substitution matrix |
delta |
gap opening penalty |
gapext |
gap extension penalty |
alignment |
type of alignment: c("global","local","overlap") |
scoring |
type of scoring, identity, similarity, score, scoreN, AAAlignemnt, pozitive |
For two objects of class AASequence
returns an object of class
AAAlignment
. Otherwise it returns a score. If used with NULL
as second parameter it
returns a distance matrix. The scores than are transformed into distances. For details see the vignette.
Witold E. Wolski witek96@users.sourceforge.net http://r4proteomics.sourceforge.net
Hilary S Booth, John H Maindonald, Ole M Nielsen, Susan R Wilson "Normalizing sequence alignment scores for composition bias" Recomb 2003 - Berlin