AAAlignment-class {pairseqsim}R Documentation

"AAAlignment" result of pairwise sequence alignment.

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 witek96@users.sourceforge.net

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)

[Package pairseqsim version 1.0.4 Index]