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HMM-Annotation-Tools

Tools that can be used for comparing ortholog groups as HMM profiles to the Pfam database.

Dependencies

Biopython

You should install Biopython before using HMMER and HHSuite.

pip install biopython

Conda

If you need to install conda for HHSuite, use the following.

conda config --add channels bioconda
conda config --add channels conda-forge
   

Usage

HMMER

To obtain HMMER releases directly from the site, visit hmmer.org for the latest release.

Download and install latest release:

wget http://eddylab.org/software/hmmer/hmmer.tar.gz
tar zxf hmmer.tar.gz
cd hmmer-3.3.2
./configure --prefix /your/install/path
make
make check                 # optional: run automated tests
make install               # optional: install HMMER programs, man pages
(cd easel; make install)   # optional: install Easel tools

HMMSearch

Use the hmmsearch.py script to run HMMER with the input MSA against Pfam.

HHSuite

HHSuite can be installed using conda as follows.

conda install -c
conda-forge -c bioconda hhsuite

HHSearch

Use the hhsuite.py script to run HHSuite with the input MSA against Pfam.