Entering edit mode
3.8 years ago
lessismore
★
1.4k
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