ProkFunFind: A pipeline to detect genes of functional interest

Overview

ProkFunFind is a pipeline that can be used to predict genes related to function of interest. Criteria for function detection include presence of gene, and genomic co-localization.

Prerequisites

• Biopython
• BLAST+
• HMMER
• InterProScan

Installation

conda create -n ProkFun python=3
conda activate ProkFun
git clone git@github.com:nlm-irp-jianglab/ProkFunFind.git
pip install ./ProkFunFind

Quick Start

prokfunfind.py -f config.yaml -gtab genome.table -o output.folder/prefix

Example Datasets

We have included multiple search configuration files from our publications that have utilized ProkFunFind to search for functions in microbial genome datasets. These search configurations can be found in the data/ directory of this ProkFunFind git repository.

To run these searches on these example set of genomes you can run the commands listed in the following table from within the respective functions directory.

Function Directory	Description	Publication (PMID)	Search command
Bilirubin_reductase	Bilirubin reductase enzyme BilR	36798240	prokfunfind -f ./config.yaml -o ./test -g ../genome-table.tsv
Cysteine_degradation	Cysteine degredation pathway	34745023	prokfunfind -f ./config.yaml -o ./test -g ../genome-table.tsv
Histidine_decarboxylase	Histidine decarboxylase	34563136	prokfunfind -f ./config.yaml -o ./test -g ../genome-table.tsv
Equol	Equol biosynthesis operon	35247986	prokfunfind -f ./config.yaml -o ./test -g ../genome-table.tsv
Flagella	Flagellar genes	TBD	prokfunfind -f ./config-{bac or pseudo}.yaml -o ./test -g ../genome-table.tsv

ProkFunAnnotate

The ProkFunAnnotate pipelile has been developed to assist in the production of the required annotation files for ProkFunFind searches. This annotation pipeline can be found in the following git repository:

• https://github.com/nlm-irp-jianglab/ProkFunAnnotate

Documentation and Tutorial

The documentation for ProkFunFind can be found here:

• https://prokfunfind.readthedocs.io/en/latest/

A tutorial describing how to run ProkFunFind searches can be found here:

• https://prokfunfind.readthedocs.io/en/docs-and-tests/tutorial/1-intro.html

Scripts

A script, gen-function-itol.py, for generated iTol tree annotation files from the TSV output of a ProkFunFind search is provided in the scripts/ directory of the ProkFunFind repository:

• https://github.com/nlm-irp-jianglab/ProkFunFind/tree/master/scripts
• This script takes the path to the ProkFunFind output directory, the character used to separate the gene from genome name, and a single column file with the feature IDs to plot as input.

Updates

• v0.1.1

  • add support for InterProScan
  • fix bug in cluster label

• v0.1.2

  • add support for InterProScan Tsv formatted output(will use tsv-formatted file in absence of xml-formatted file)

• v0.2.0

  • add support for pangenome

• v0.2.1

  • fix system.json process error and modify pangenome for speed improvement

• v0.2.2

  • add support for kofam