featureDOMAIN {BioSeqClass} | R Documentation |
Protein sequences are coded based on their domains.
featureDOMAIN(domain) # Protein Pfam domain prediction predictPFAM(seq, hmmpfam.path, pfam.path, Evalue=10^-5)
domain |
a list of protein domains. It can be produced by function
|
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. |
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.
Hong Li
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