BioSeqClass (version 1.30.0)

featureDOMAIN: Feature Coding by doamin organization

Description

Protein sequences are coded based on their domains.

Usage

featureDOMAIN(domain)  # Protein Pfam domain prediction predictPFAM(seq, hmmpfam.path, pfam.path, Evalue=10^-5)

Arguments

domain

a list of protein domains. It can be produced by function predictPFAM.

seq

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

hmmpfam.path

a string for the path of hammpfam program in HMMER. hammpfam will be employed to predict domains using models in Pfam database.

pfam.path

a string for the path of pfam domain database.

Evalue

a numeric value for the E-value cutoff of perdicted Pfam domain.

Details

featureDOMAIN uses Pfam domains to code 0-1 feature vector. predictPFAM predict Pfam domains by hmmpfam program. It returns a list, each element is a vector which denotes the domain composition of a protein.

Examples

if(interactive()){

}