Introduction

HMMER is a bioinformatics program designed to take in genetic sequences and and search for homologs in genetic databases and computes sequence alignments. The program uses probabilistic profile Hidden Markov Models for much of its computational work.

Using HMMER on RCC Resources

HMMER does not require a particular module to be loaded on RCC systems and can be run straight after logging in. There are a number of programs included in HMMER including hmmalign, hmmbuild and more. For a complete listing and a tutorial on usage, see the documentation. On HPC systems, HMMER can be run by the following commands:

HMMER_PROGRAM -OPTIONS INFILES OUTFILES
# HMMER_PROGRAM is one of hmmalign, hmmbuild, nhmmer or any other from the listing

Running HMMER in Parallel

In order to run HMMER programs in parallel, you'll need one of the OpenMPI modules such as gnu-openmpi.  The programs from the HMMER package can then be run in parallel by running the commands:

module load gnu-openmpi
mpirun -np N HMMER_PROGRAM -OPTIONS INFILES OUTFILES
# HMMER_PROGRAM is one of hmmalign, hmmbuild, nhmmer or any other from the listing