BioSeqClass (version 1.30.0)

featureDIPRODB: Feature Coding by Dinucleotide Property

Description

Sequences are coded by conformational or thermodynamic dinucleotide property from DiProDB database.

Usage

featureDIPRODB(seq, na.type="all", na.strand="all", diprodb.method="all",  diprodb.type="all")

Arguments

seq

a string vector for the protein, DNA, or RNA sequences.

na.type

a string for nucleic acid type. It must be "DNA", "DNA/RNA", "RNA", or "all".

na.strand

a string for strand information. It must be "double", "single", or "all".

diprodb.method

a string for mode of property determination. It can be "experimental", "calculated", or "all".

diprodb.type

a string for property type. It can be "physicochemical", "conformational", "letter based", or "all".

Details

featureDIPRODB returns a matrix with 122 columns. Each column is the mean of conformational or thermodynamic dinucleotide property from DiProDB database (http://diprodb.fli-leibniz.de).

Examples

if(interactive()){
  file = file.path(path.package("BioSeqClass"), "example", "test.rna")    
  rna = as.matrix(read.csv(file,header=F,sep="\t"))[,1]
  
  DIPRODB1 = featureDIPRODB(rna)
  DIPRODB2 = featureDIPRODB(rna, na.type="RNA")
}