Microbial 'omics


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anvi-3dev: Integrating metagenomic sequence variants and predicted protein structures

anvi-3dev is an analysis and visualization platform for visualizing single-amino acid and single-codon variants derived from metagenomic/metatranscriptomic data onto predicted protein structure. 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 ecoogy and structural biology.

Install

anvi-3dev is developed using the anvi’o framework. In fact, it is integrated directly into anvi’o, which means installing anvi-3dev is installed by installing anvi’o.

How to cite

If you use anvi-3dev, please cite this paper.

Kiefl E, Esen ÖC, Eren AM (2020) anvi-3dev: integrating metagenomic sequence variants and predicted protein structures. (in preparation)

Made possible by

Like all software, anvi-3dev is built upon other software, all of which is open source. It is especially indebted to the following list of projects, without which anvi-3dev 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-3dev

Infant Gut Tutorial

A comprehensive tutorial on anvi'o features, with a section dedicated to anvi-3dev.