annotate_pfam: Annotate proteins sequences with PFAM domains

In almeidasilvaf/tfhunter: Identification and classification of plant transcription factors

Annotate proteins sequences with PFAM domains

Description

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)
}

almeidasilvaf/tfhunter documentation built on March 19, 2023, 8:53 p.m.