AAAlignment-class: "AAAlignment" result of pairwise sequence alignment.

In wolski/pairseqsim: pairwise sequence alignment similarity simple.

Description

Result of a pairwise sequence alignment.

Objects from the Class

Objects can be created by calls of the form new("AAAlignment", ...).

Slots

info1:

Object of class "character" : name of first sequence.

info2:

Object of class "character" : name of second sequence

selfs1:

Object of class "numeric" : selfscore of sequence 1

selfs2:

Object of class "numeric" : selfscore of sequence 2

score:

Object of class "numeric" : Smith Watermann score of alignment.

identity:

Object of class "numeric" : nr of identitacal AA in the alignment.

alignsimilarity:

Object of class "numeric" : nr of similarities.

lch1:

Object of class "numeric" : length of sequence 1.

lch2:

Object of class "numeric" : length of sequence 2

alig1:

Object of class "character" : alignment string

alig2:

Object of class "character" : alignment string

beautify:

Object of class "character" : internal

Methods

show

signature(object = "AAAlignment"): show

summary

signature(object = "AAAlignment"): summary

Author(s)

Witold E. Wolski [e-mail]

References

http://r4proteomics.sourceforge.net

See Also

salign-methods

Examples

data(EBLOSUM62)
seq1<-new("AASequence","MEDQVGFGFRPNDEEL",info="seq1")
seq2<-AASequence("seq1","VAISEVNICSYDPWNL")
res<-salign(seq1,seq2,EBLOSUM62,delta=-10,gapext=-1,alignment="global")
class(res)
summary(res)

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