Dear,

i am using bio3d to scan an input set of sequences for PFAM profiles. For this i simply use this code

test <- read.fasta("/home/test.fa")
result <- hmmer(test, type = "hmmscan", db = "pfam")

What i want to achieve is the same output that you can obtain by https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan i.e.uploading a multifasta sequence file and getting all this information.

 Sequence Number    Query Name  Hits Found  Status  Top Hit Details

Am i missing something with the code? thank for any help. If it's not possible to achieve this, is there an alternative?

Thanks