AASequence-class {pairseqsim}R Documentation

"AASequence" Object representation of a protein Sequence

Description

Object representation of a protein Sequence

Objects from the Class

Objects can be created by calls of the form new("AASequence", sequence, info, alphabet). or by call to AASequence("PROTINSEQUENCEHERE",info="my prot seq")

Slots

.Data:
Object of class "character" the sequence
info:
Object of class "character" the info

Extends

Class "character", directly.

Methods

frequency
signature(x = "AASequence"): returns the amino acid frequencies
initialize
signature(.Object = "AASequence"): internal
readFasta
signature(object = "AASequence"): read FASTA file format
salign
signature(obj1 = "AASequenceList", obj2 = "AASequence"): see: salign-methods
salign
signature(obj1 = "AASequence", obj2 = "AASequenceList"): see: salign-methods
salign
signature(obj1 = "AASequence", obj2 = "AASequence"): see: salign-methods
selfalign
signature(object = "AASequence", sub = "Submatrix"): Computes Smith-Waterman score of the alignment of the sequence with itself.
show
signature(object = "AASequence"):
testalign
signature(obj1 = "AASequence", obj2 = "AASequence"): internal, see: testalign-methods

Author(s)

Witold E. Wolski witek96@users.sourceforge.net

References

http://r4proteomics.sourceforge.net

See Also

salign-methods,readFasta-methods

Examples

seq1<-new("AASequence","MEDQVGFGFRPNDEEL",info="seq1")
seq2<-AASequence("seq2","VAISEVNICSY")

[Package pairseqsim version 1.0.4 Index]