featureDOMAIN: Feature Coding by doamin organization

In BioSeqClass: Classification for Biological Sequences

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

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BioSeqClass documentation built on April 28, 2020, 9:19 p.m.