Prediction of bacterial amino acid auxotrophy

Project to predict amino acid biosynthesis capabilities across the bacterial tree of life and to investigate associated life history strategies. This repository contains the data and code required to annotate genomes into amino acid biosynthesis pathways using the annotation tool GapMind (https://doi.org/10.1128/msystems.00291-20) and to replicate the figures in the original publication. For the full list of amino acid biosynthesis predictions across the >26,000 genomes included in the study please see file 2022-10-09_bacteria_auxotrophies_subset_all.txt.

本项目旨在预测整个细菌生命树中的氨基酸生物合成能力，并探究相关的生命史策略。本仓库包含所需的数据与代码，可借助注释工具GapMind（https://doi.org/10.1128/msystems.00291-20）将基因组注释至氨基酸生物合成通路中，同时可复现原发表论文中的图表。若需获取本研究中纳入的逾26000个基因组的全部氨基酸生物合成预测结果，请查看文件2022-10-09_bacteria_auxotrophies_subset_all.txt。