Annotate proteins sequences with PFAM domains — annotate

PFAM domains are assigned to each sequence using HMMER.

Usage

annotate_pfam(seq = NULL, evalue = 1e-05)

Arguments

seq: An AAStringSet object as returned by Biostrings::readAAStringSet(). The sequences in this object must represent only the translated sequences of primary (or longest) transcripts.
evalue: Numeric indicating the E-value threshold for hmmsearch to be used for domains without pre-defined domain cutoffs. Only valid if parameter mode = 'local'. Default: 1e-05.

Value

A 2-column data frame with the variables Gene

and Domain, which contain gene IDs and domain IDs, respectively.

Examples

data(gsu)
seq <- gsu[1:5]
if(hmmer_is_installed()) {
    annotate_pfam(seq)
}
#>         Gene  Domain
#> 1 gsu06140.1 PF00249
#> 2 gsu05000.1 PF02042
#> 3 gsu04730.1 PF02042
#> 4 gsu00340.1 PF00076
#> 5 gsu06140.1 G2-like