| AAAlignment-class {pairseqsim} | R Documentation |
Result of a pairwise sequence alignment.
Objects can be created by calls of the form new("AAAlignment", ...).
info1:"character" : name of
first sequence. info2:"character" : name of
second sequence selfs1:"numeric" : selfscore
of sequence 1 selfs2:"numeric" : selfscore
of sequence 2score:"numeric" : Smith
Watermann score of alignment. identity:"numeric" : nr of
identitacal AA in the alignment.alignsimilarity:"numeric" : nr
of similarities.lch1:"numeric" : length of
sequence 1.lch2:"numeric" : length of
sequence 2 alig1:"character" : alignment string alig2:"character" : alignment string beautify:"character" :
internal signature(object = "AAAlignment"): show signature(object = "AAAlignment"): summary Witold E. Wolski
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)