-
Notifications
You must be signed in to change notification settings - Fork 23
hmmer_seq
Martin Asser Hansen edited this page Oct 2, 2015
·
6 revisions
hmmer_seq uses HMMER to search for protein motifs in peptide sequeces in the stream using a specified database of motif models.
The resulting records look like this:
REC_TYPE: HMMER
S_ID: test
S_AC: -
Q_ID: HORMA
Q_AC: PF02301.13
E_VAL_SEQ: 5.8e-27
SCORE_SEQ: 80.9
BIAS_SEQ: 3.6
E_VAL_DOM: 7.4e-27
SCORE_DOM: 80.5
BIAS_DOM: 2.5
EXP: 1.1
REG: 1
CLU: 0
OV: 0
ENV: 1
DOM: 1
REP: 1
INC: 1
DESC: -
---
HMMER v. 3.0 or later must be installed for hmmer_seq to work. Read more about HMMER here:
... | hmmer_seq [options] -d <index>
[-? | --help] # Print full usage description.
[-d <file!> | --database=<file!>] # Database file with motifs.
[-c <uint> | --cpus=<uint>] # Number of CPUs to use - Default=1
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
To locate the protein domains in the sequences in the FASTA file test.faa using hmmer_seq do:
read_fasta -i test.faa | hmmer_seq -d $BP_DATA/Pfam/Pfam-A.hmm
Martin Asser Hansen - Copyright (C) - All rights reserved.
May 2012
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
hmmer_seq is part of the Biopieces framework.