MHCscan

Software tool for identification of multiheme cytochromes

Install Miniconda

Installation

git clone https://github.com/Arkadiy-Garber/MHCscan/tree/main
conda create -n mhcscan -c bioconda -c conda-forge -c defaults hhsuite prodigal --yes

Put MHCscan main repo and bin into your PATH variable

export PATH="/path/to/MHCscan:$PATH"
export PATH="/path/to/MHCscan/bin:$PATH"

(recommended to add this to your .bashrc, .bash_profile, .profile, or .zshrc scripts)

Download databases for hhsuite

We recommend using PDB70, which can be downloaded with the following command (make sure you have > 60 Gb of free storage space)

wget https://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/pdb70_from_mmcif_latest.tar.gz

Usage (with annotated genome)

MHCscan.sh -i proteins.faa -g annotation.gff -o output.csv -t 16 --prot

Usage (with unannotated genome)

MHCscan.sh -i contigs.fasta -o output.csv -t 16