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)