BioFung allows fungi specific annotation for function and insight into pathways (please see manuscript for more details). It a database that allows comprehensive information on the metabolism of fungal species.
This database is described in-depth within the manuscript, can be found at __________. BioFung allows fungi specific annotation for function and insight into pathways (please see manuscript for more details). It a database that allows comprehensive information on the metabolism of fungal species.
BioFung has been built and used on LINUX/MacOS system. Requirements: Java 7 or 8
Users can download BioFung.hmm to use independently by operating with HMMER software. We have included instructions for use of BioFung both on a cluster or locally. BioFung workflow has been placed into Nextflow integrated with Docker and HMMER. Instruction of Nextflow and Docker installation is below
Docker engine 1.10.x (or higher) Install docker: https://docs.docker.com/engine/install/
Nextflow installation guide can be found: https://www.nextflow.io/
Check that you have correct Java version for nextflow java -version
Create a nextflow directory in your directory if not already done so. curl -s https://get.nextflow.io | bash
Launch with a demo ./nextflow run hello
The above snippet creates the nextflow launcher in the current directory. Complete the installation moving it into a directory on your PATH eg: mv nextflow $HOME/bin
Finally, clone this repository with the following command: git clone https://github.com/NeeluBegum/BioFung.git && cd BioFung/nextflow-version
#download repository git clone https://github.com/NeeluBegum/BioFung.git
Run it by using the following command: ./nextflow run main.nf --input ../afumigatus.fasta
#check nextflow progress ./nextflow log
#check progress of nextflow for mac users in brewer tree --du -h
The BioFung database "BioFung.hmm" is (file size: 1.41GB). The input data requires protein fasta data. the output includes list of protein-encoding gene, KEGG ortholog, evalue matching and corresponding identification of KEGG orthologs. This text file then can be used for annotation of metabolic pathway using the KEGG database (https://www.genome.jp/kegg/pathway.html).
#check for nexflow installation at https://github.com/nf-core/configs for example, KCL rosalind : https://github.com/nf-core/configs/blob/master/docs/rosalind.md
module load apps/openjdk module load apps/singularity
wget https://github.com/nextflow-io/nextflow/releases/download/v21.04.3/nextflow-21.04.3-all chmod a+x nextflow-21.04.3-all mv nextflow-21.04.3-all ~/bin/nextflow
###installtion guide for git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
git clone https://github.com/NeeluBegum/BioFung scp /Users/your_path/Biofung HPC:/your_path/
Nextflow installation guide can be found: https://www.nextflow.io/
Check that you have correct Java version for nextflow java -version
Create a nextflow directory in your directory if not already done so. curl -s https://get.nextflow.io | bash
Launch with a demo ./nextflow run hello
The above snippet creates the nextflow launcher in the current directory. Complete the installation moving it into a directory on your PATH eg: mv nextflow $HOME/bin
Clone this repository with the following command: git clone https://github.com/NeeluBegum/BioFung
Run it by using the following command: ./nextflow run BioFung/nextflow-version/main.nf --input Biofung/afumigatus.fasta
#check nextflow progress ./nextflow log
example: result.tsv should include KO hits for your sequence.
KAF4289899.1 K00002 4.1e-07 KAF4283082.1 K00002 7.5e-07 KAF4291635.1 K00002 7.5e-07 KAF4289968.1 K00002 1.1e-06 KAF4282554.1 K00003 5.1e-163 KAF4294980.1 K00003 5.1e-163 KAF4283344.1 K00004 3.8e-58
checking the KEGG database determines K00003 is for amino acid metabolism https://www.genome.jp/dbget-bin/www_bget?ko:K00003. With the translation of the information can be used to plot metabolic information of fungal species as shown in manuscript but additional use of BioFung can be demonstrated with aspergillus in Supplementary1 figure.
Contributing: Created by Begum N. based on KEGG annotations Contact: neelu.begum@kcl.ac.uk
Acknowledgements: Theo Portlock SysbiomeLab Nextflow Docker KEGG HMMER
Please checkout main group page for updated code: sysbiomelab/BioFung
check out BioFung on https://github.com/sysbiomelab for information and you can download BioFung from https://www.microbiomeatlas.org/downloads.php
Find out more about our research team on: https://www.sysbiomelab.com/ and my co-lab: https://www.kcl.ac.uk/research/functional-microbiome-group-moyes-group