featureDOMAIN {BioSeqClass} | R Documentation

## 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.

### Author(s)

Hong Li

### Examples

    if(interactive()){

    }

[Package BioSeqClass version 1.40.0 Index]