KofamScan Workflow

Analysis
Functional annotation
Published

March 23, 2023

Analysis·Tools KofamScan

This post is inspired by E. Chille’s and D. Becker’s posts on genomic functional annotations.

Map KEGG terms to genome

KofamScan is the command-line version of the popular KofamKOALA web-based tool, used to map Kegg terms (containing pathway information) to a genes. KofamScan and KofamKoala work by using HMMER/HMMSEARCH to search against KOfam (a customized HMM database of KEGG Orthologs (KOs). Mappings are considered robust because each Kegg term has an individual pre-defined threshold that a score has to exceed in order to map to a gene. While all mappings are outputted, high scoring (significant) assignments are highlighted with an asterisk.

The commands that I used are below. In order to run KofamScan, you will need a fasta file of predicted protein sequences (preferably the same one used to run InterProScan).

General Protocol:

1. Download and inflate the Kofam database

To get the most up-to-date Kofam database, download it just before running KofamScan. You will also need to download the profiles associated with the Kofam database containing threshold information.

cd /nethome/kxw755/opt
curl -O ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz  #download and unzip KO database
curl -O ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz  #download and inflate profiles

gunzip ko_list.gz
tar xf profiles.tar.gz

Downloaded 20230323

Install Anaconda on pegasus (only if you have not done this before):

wget https://repo.anaconda.com/archive/Anaconda3-2021.05-Linux-x86_64.sh
bash Anaconda3-2021.05-Linux-x86_64.sh
source /nethome/kxw755/anaconda3/bin/activate

Installed 20230323

Install KofamScan:

cd /nethome/kxw755/opt/
conda install -c bioconda kofamscan

something did not install correctly here. Need to revisit

I am going to excute this on andromeda instead

mkdir kofamscan
cd ../../data/putnamlab/kevin_wong1/kofamscan

curl -O ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz  #download and unzip KO database
curl -O ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz  #download and inflate profiles

gunzip ko_list.gz
tar xf profiles.tar.gz

Downloaded 20230323

Installed 20230323

2. Run KofamScan

Download Mnemi protein file:

wget https://research.nhgri.nih.gov/mnemiopsis/download/proteome/ML2.2.aa.gz
gunzip ML2.2.aa.gz

nano kofamscan_ML.sh

#!/bin/bash
#SBATCH --job-name="KofamScan"
#SBATCH -t 30-00:00:00
#SBATCH --export=NONE
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=kevin_wong1@uri.edu
#SBATCH --nodes=1 --ntasks-per-node=20
#SBATCH --mem=100GB
#SBATCH -D /data/putnamlab/kevin_wong1/kofamscan

echo "Loading modules" $(date)
module load kofam_scan/1.3.0-foss-2019b
module load libyaml/0.1.5
module unload HMMER/3.3.1-foss-2019b
module load HMMER/3.3.2-gompi-2019b
module list

#echo "Starting analysis... downloading KO database" $(date)
#wget ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz #download KO database
#wget ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz
#gunzip ko_list.gz
#tar xf profiles.tar.gz

echo "Beginning mapping" $(date)
/opt/software/kofam_scan/1.3.0-foss-2019b/exec_annotation \
-o Mnemi_KO_annot.txt \
-k ./ko_list \
-p ./profiles/eukaryote.hal \
-E 0.00001 \
-f detail-tsv \
--report-unannotated ./ML2.2.aa


echo "Analysis complete!" $(date)
scp -r kevin_wong1@ssh3.hac.uri.edu:/data/putnamlab/kevin_wong1/kofamscan/Mnemi_KO_annot.txt /Users/kevinwong/MyProjects/Mnemi_Phagocyte/output/KofamScan/Mnemi_KO_annot.txt
Back to top