salign-methods {pairseqsim} | 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
data(sequlist) data(EPAM110) #example of alignment res<-salign(sequlist[[1]],sequlist[[2]],EPAM110,delta=-4,gapext=-1,alignment="global") summary(res) #scoring a sequence against a list of sequences. res <- salign( sequlist[1:10] , sequlist[[1]], EPAM110 , delta = -4,gapext = -1,alignment = "local", scoring = "score") hist(res) #computing a distance matrix. res<-salign(sequlist[1:10],NULL,EPAM110,delta=-10,gapext=-1,alignment="overlap",scoring="pozitive") hist(as.numeric(res))