AASequence-class: "AASequence" Object representation of a protein Sequence

In wolski/pairseqsim: pairwise sequence alignment similarity simple.

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 [e-mail]

References

http://r4proteomics.sourceforge.net

See Also

salign-methods,readFasta-methods

Examples

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

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