Abstract
There is an increasing availability of complete or draft genome sequences for microbial organisms. These data form a potentially valuable resource for genotype-phenotype association and gene function prediction, provided that phenotypes are consistently annotated for all the sequenced strains. In this review, we address the requirements for successful gene-trait matching. We outline a basic protocol for microbial functional genomics, including genome assembly, annotation of genotypes (including single nucleotide polymorphisms, orthologous groups and prophages), data pre-processing, genotype-phenotype association, visualization and interpretation of results. The methodologies for association described herein can be applied to other data types, opening up possibilities to analyze transcriptome-phenotype associations, and correlate microbial population structure or activity, as measured by metagenomics, to environmental parameters.
| Original language | English |
|---|---|
| Article number | elt008 |
| Pages (from-to) | 366-380 |
| Number of pages | 15 |
| Journal | Briefings in Functional Genomics |
| Volume | 12 |
| Issue number | 4 |
| DOIs | |
| Publication status | Published - Jul 2013 |
| Externally published | Yes |
Bibliographical note
The Author 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Keywords
- Functional genomics
- Genome-wide association studies
- Genotype-phenotype association
- Microbial genomics
- Random forest