salign-methods: Optimal pairwise alignment of two protein sequences.

In wolski/pairseqsim: pairwise sequence alignment similarity simple.

Description

Computes optimal pairwise alignment of 2 protein sequences.

Arguments

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

Value

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.

Methods

obj1 = "AASequenceList", obj2 = "NULL"

Compute distance matrix.

obj1 = "AASequenceList", obj2 = "AASequence"

Compute scores.

obj1 = "AASequence", obj2 = "AASequenceList"

Compute scores.

obj1 = "AASequence", obj2 = "AASequence"

Compute alignment.

Author(s)

Witold E. Wolski [e-mail] http://r4proteomics.sourceforge.net

References

Hilary S Booth, John H Maindonald, Ole M Nielsen, Susan R Wilson "Normalizing sequence alignment scores for composition bias" Recomb 2003 - Berlin

Examples

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))

wolski/pairseqsim documentation built on May 4, 2019, 9:47 a.m.