Integrating sequence variants and predicted protein structures (Tue, Sep 04, 2018)
A discussion on the practical and theoretical aspects of using anvi'o structure
Anvi’o structure: Integrating metagenomic sequence variants and predicted protein structures
Anvi’o structure is an integrated component of anvi’o focused on the analysis and visualization of single-amino acid and single-codon variants derived from metagenomic/metatranscriptomic data in the context of predicted protein structures and binding sites. Its purpose is to enable microbial ecologists with the tools necessary to investigate microbial diversity within the context of the structural properties of translated gene products, thereby bridging a gap between microbial ecology and structural biology.
Install
Anvi’o structure is an integrated part of the anvi’o framework. By installing anvi’o, you are installing everything that makes up anvi’o structure, as well.
How to cite
If you use anvi’o structure, please cite this paper:
Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution
📚 Science Advances, 9(8):eabq4632 | 🔍 Google Scholar | 🔗 doi:10.1126/sciadv.abq4632
- A study that describes an approach to integrate environmental microbiology with recent advances in protein structure prediction, and illustrates the tight association between intra-population genetic variants, environmental selective pressures, and structural properties of proteins.
- Demonstrates a quantifiable link between (1) the magnitude of selective pressures over key metabolic genes (e.g., glutamine synthase of the central nitrogen metabolism), (2) the availability of key nutrients in the environment (e.g., nitrate), and (3) the maintenance of nonsynonymous variants near protein active sites.
- Shows that the interplay between selective pressures and protein structures also maintains synonymous variants -- revealing a quantifiable link between translational accuracy and fluctuating selective pressures.
- Comes with a reproducible bioinformatics workflow that offers detailed access to computational steps used in the study that spans from metagenomic read recruitment and profiling to the integration of environmental variants and predicted protein structures.
- Demonstrates a quantifiable link between (1) the magnitude of selective pressures over key metabolic genes (e.g., glutamine synthase of the central nitrogen metabolism), (2) the availability of key nutrients in the environment (e.g., nitrate), and (3) the maintenance of nonsynonymous variants near protein active sites.
- Shows that the interplay between selective pressures and protein structures also maintains synonymous variants -- revealing a quantifiable link between translational accuracy and fluctuating selective pressures.
- Comes with a reproducible bioinformatics workflow that offers detailed access to computational steps used in the study that spans from metagenomic read recruitment and profiling to the integration of environmental variants and predicted protein structures.
Made possible by
Like all software, anvi’o structure is built upon other software, all of which is open source. It is especially indebted to the following list of projects, without which anvi’o structure would not have been developed:
MODELLER
Citation: doi:10.1002/0471250953.bi0506s15
Citation: doi:10.1146/annurev.biophys.29.1.291
Citation: doi:10.1006/jmbi.1993.1626
MODELLER is the program anvi’o uses to predict protein structure based on experimentally solved structures in the Protein Data Bank. We’ll talk more specifically about how it accomplishes this in the following section, but for now you need to make sure it’s installed on your computer. For that, check out these instructions to see if you have it installed (click me), and how to install it if you don’t. We’ve tried to make it as simple for you as possible.
NGL
Citation: doi:10.1093/nar/gkv402
Citation: doi:10.1093/bioinformatics/bty419
NGL (NGL) is an open-source project for visualizing biomolecules. This browser-based solution to visualization means you don’t have to install anything, and you can thank them for that. Özcan has been the mastermind behind incorporating NGL’s visualizations into anvi’o, and says he continues to be impressed with their excellent code, documentation, and open-source approach to science.
Posts and tutorials about anvi’o structure
Infant Gut Tutorial
A comprehensive tutorial on anvi'o features, with a section dedicated to anvi'o structure.