Apr 16, 2020
The calculation of gut metabolic modules form gene profile
- 1BGI
- GigaScience Press
- BGI
Protocol Citation: Qi Wang 2020. The calculation of gut metabolic modules form gene profile. protocols.io https://dx.doi.org/10.17504/protocols.io.be7ajhie
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 16, 2020
Last Modified: April 16, 2020
Protocol Integer ID: 35778
Keywords: gut metabolic modules, Metagenomics data, KO profile,
Abstract
The calculation of gut metabolic modules form gene profile
Guidelines
The calculation of gut metabolic modules form gene profile
Before start
The input is the gene profile
Step 1: the putative amino acid sequences were translated from the gene catalogues and aligned against the proteins/domains in the KEGG databases (release 79.0, with animal and plant genes removed) using BLASTP (v2.2.26, default parameter except that -e 0.01 -b 100 -K 1 -F T -m 8). Each protein was assigned to the KO group by the highest scoring annotated hit(s) containing at least one HSP scoring >60 bits.The relative abundance profile of KOs was determined by summing the relative abundance of genes from each KO.
Step 2: The calculation of gut metabolic modules by one command:
'java -jar gmms.jar -a 2 -d GMMs.v1.07.txt -i input_KO_profile -s average -o index'