salign-methods {pairseqsim} R Documentation

## Optimal pairwise alignment of two protein sequences.

### 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 witek96@users.sourceforge.net 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))
```

[Package pairseqsim version 1.0.4 Index]