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Profile hidden Markov models for biological sequence analysis

Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER uses profile HMMs, and can be useful in situations like:

• if you are working with an evolutionarily diverse protein family, a BLAST search with any individual sequence may not find the rest of the sequences in the family.
• the top hits in a BLAST search are hypothetical sequences from genome projects.
• your protein consists of several domains which are of different types.

References:

HMMER (pronounced 'hammer', as in a more precise mining tool than BLAST) was developed by Sean Eddy at Washington University in St. Louis.

• The HMMER website is hmmer.janelia.org.
• HMMER User Guide (PDF)
  

• Module Name: hmmer (see the modules page for more information)
• HMMER is a cpu-intensive program and is parallelized using threads, so that each instance of hmmsearch or the other search programs can use all the cpus allocated on a node.
• An MPI version is also available, but given that most Biowulf nodes have 56 CPUs, only very large jobs may benefit from using the MPI version.
• environment variables set
• Example files in /usr/local/apps/hmmer/tutorial
• Reference data in /fdb/fastadb/

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=16 --mem=10g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load hmmer

[user@cn3144 ~]$ hmmsearch --cpu $SLURM_CPUS_PER_TASK /usr/local/apps/hmmer/tutorial/globins4.hmm /fdb/fastadb/nr.fas
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.1b2 (February 2015); http://hmmer.org/
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  /usr/local/apps/hmmer/tutorial/globins4.hmm
# target sequence database:        /fdb/fastadb/nr.fas
# number of worker threads:        16
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       globins4  [M=149]
[...]
  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 0.0014
        globins4  41 qefFekFkdLstedelkksadvkkHgkkvldAlsdalakld..ekleaklkdLselHakklkvdpkyfkllsevlvdvlaarlpkeftadvqaal 133
                     q++F++  +L+   ++   +     g+ + +A+++  +++d  + l ++++ ++++H ++++++ ++++++++ l+++l +  +  ft dv+ a
  WP_087017392.1  30 QRMFDHNPELKDIFNMSH-QRTGRQGVALFEAVAAYAKNIDnlGALTTAVERIAHKH-TSFNIQAEHYQIVGHHLIETLRELASDAFTKDVEEAW 122
                     677777777873333333.3345679999***********87889999*********.58*******************************9886 PP

        globins4 134 e 134

  WP_087017392.1 123 T 123
                     5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                              1  (149 nodes)
Target sequences:                    145198384  (53182534605 residues searched)
Passed MSV filter:                   4463369  (0.0307398); expected 2903967.7 (0.02)
Passed bias filter:                  3672241  (0.0252912); expected 2903967.7 (0.02)
Passed Vit filter:                    255552  (0.00176002); expected 145198.4 (0.001)
Passed Fwd filter:                     17247  (0.000118782); expected 1452.0 (1e-05)
Initial search space (Z):          145198384  [actual number of targets]
Domain search space  (domZ):           10862  [number of targets reported over threshold]
# CPU time: 1306.00u 76.30s 00:23:02.30 Elapsed: 00:11:03.54
# Mc/sec: 11942.31

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. HMMER.sh). The following example uses the query sequence set globins4.hmm in the example directory, run against the NCBI nr protein database.

#!/bin/bash
set -e
module load hmmer
hmmsearch --cpu $SLURM_CPUS_PER_TASK /usr/local/apps/hmmer/tutorial/globins4.hmm /fdb/fastadb/nr.fas

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=10g HMMER.sh

Create a swarmfile (e.g. HMMER.swarm). For example:

hmmsearch --cpu $SLURM_CPUS_PER_TASK  file1.fas  /fdb/fastadb/nr.fas
hmmsearch --cpu $SLURM_CPUS_PER_TASK  file2.fas  /fdb/fastadb/nr.fas
hmmsearch --cpu $SLURM_CPUS_PER_TASK  file3.fas  /fdb/fastadb/nr.fas
[...]

Submit this job using the swarm command.

swarm -f HMMER.swarm -g 10 -t 32 --module hmmer

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t #	Number of threads/CPUs required for each process (1 line in the swarm command file).
--module hmmer	Loads the HMMER module for each subjob in the swarm