GRINS: Genetic elements that recode assembly-line polyketide synthases and accelerate their diversification

This repository contains code asssociated with the following publication.

Please cite the code in this repository with the following:

Nivina A, Herrera Paredes S, Fraser H & Khosla C. "GRINS: genetic
elements that recode assembly-line polyketide synthases and
accelerate their diversification". PNAS June 29, 2021 118 (26) e2100751118;
https://doi.org/10.1073/pnas.2100751118

Directories

• annotations: Code to annotate genomes.

• checkm: Code to run checkM.

• detection: Code to detect GRINS.

• phylo: Code for phylogenetic analysis.

• conda_envs: Conda environment .yml files to recreate the environments in the publication.

Detecting GRINS

Instructions for running the code used to predict GRINS in novel genomes are in the detection directory. Bear in mind that the current workflow requires unannotated fasta assemblies as input, and performs de-novo annotation.

Copyright & License

(C) Copyright 2017-2021 Sur Herrera Paredes, Aleksandra Nivina

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.