Get full output with hmmscan in bio3d
0
0
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

bio3d • 634 views
ADD COMMENT

Login before adding your answer.

Traffic: 1710 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6