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Introduction
HMMER is a popular open source implementation of profile Hidden Markov Models (HMM) algorithm, widely used for sequence analysis of bio-molecules. It is often used together with profile databases like, Pfam (for protein families), Rfam (for non-coded RNA families), Dfam (for repetitive DNA based), etc. It is developed and maintained by Prof. Sean Eddy (Harvard University).
Official Website for HMMER: https://hmmer.org/
Build HMMER using Spack
Reference to add external packages to Spack: Build Customization (Adding external packages to Spack)
# Format For Building HMMER with AOCC$ spack -d install -v hmmer@<Version> +mpi %aocc@<Version> ^openmpi@<Version> |
# Example: For building HMMER 3.3.2 with AOCC 3.2.0$ spack -d install -v -j 16 hmmer@3.3.2 +mpi %aocc@3.2.0 ^openmpi@4.1.1 |
Use any combination of following components/applications and their versions:
| Component/Application | Versions Applicable |
| HMMER | 3.3.2, 3.3, 3.2.1, 3.0 |
| AOCC | 3.2.0, 3.1.0, 3.0.0, 2.3.0, 2.2.0 |
Specifications and Dependencies
| Symbol | Meaning |
| -d | To enable debug |
| -v | To enable verbose |
| -j 16 | To enable parallel build |
| @ | To specify version number |
| % | To specify compiler |
| +mpi | Compile with MPI |
| ^openmpi | Build with Open MPI |
Running HMMER
| Program | Description |
| hmmbuild | Build profile from input multiple alignment |
| hmmsearch | Search profile against sequence database |
| hmmscan | Search sequence against profile database |
| hmmalign | Make multiple sequence alignment using a profiler |
The following example illustrates the usage of hmmsearch using Pfam database and uniprot_sprot as the input:
| Setting Environment |
# Format for loading HMMER build with AOCC$ spack load hmmer@<Version> %aocc@<Version> |
# Example: Load HMMER build with AOCC 3.2.0 module into environment$ spack load hmmer@3.3.2 %aocc@3.2.0 |
| Obtaining Input Files |
# Pfam Database$ wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz$ unzip -d Pfam-A.hmm.gz |
# uniprot_sprot.fasta input$ wget https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz$ unzip -d uniprot_sport.fasta.gz |
| Running hmmsearch |
$ mpirun -np 128 hmmsearch --mpi -o hmmsearch.out Pfam-A.hmm uniprot_sprot.fasta |