水平基因转移HGT

文献代表

标题：Elevated rates of horizontal gene transfer in the industrialized human microbiome
中文：非工业地区人体微生物组水平基因转移提高
杂志：CELL
时间：2021
单位：剑桥麻省理工
HGT定义：
We used Blast (blastn, v2.6.0) to systematically detect blocks of DNA that are shared by two genomes of different species. We retained blast hits with 100% similarity and that are larger than 500bp.

标题：Mobile genes in the human microbiome are structured from global to individual scales
中文：人体微生物群的移动基因
杂志：Nature
时间：2016
单位：剑桥哈佛麻省理工
HGT定义：
Recent DNA transfers are defined as the presence of near-identical DNA fragments (99% percent identity or greater) with a length of 500 basepairs or greater in two distantly related genomes.

检测方法

HGTector2

标题：HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers
杂志：BMC bioinformatics
时间：2014
引用：60 (2021.9)

Github：https://github.com/qiyunlab/HGTector

1 软件获取

conda create -n HGTector
conda activate HGTector
conda install python=3 pyyaml pandas matplotlib scikit-learn bioconda::diamond

#pip install git+https://github.com/qiyunlab/HGTector.git
git clone https://github.com/qiyunlab/HGTector.git
cd HGTector
python setup.py install 
# --user  # 该参数会把软件安装在Home，家小勿用

2 获取数据库

./hgtector database -o /route/database/HGTector/ \
--default

OSError: [Errno 122] Disk quota exceeded

Blastn

#建库
makeblastdb -in db_blast/total.ffn \
-input_type fasta -dbtype nucl -title total -parse_seqids \
-out db_blast/total

#比对一个基因组
blastn -db ./db_blast/total \
-outfmt 6 \
-max_target_seqs 100000000 \
-num_threads 4 \
-perc_identity 100 \
-evalue 1e-6 \
-query ./genome/T2103096366.ffn \
-out ./out/T2103096366_blast.out

MetaCHIP

标题：MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches
中文：群落水平HGT鉴定方法
杂志：Microbiome
时间：2019
单位：新南威尔士大学

Github: https://github.com/songweizhi/MetaCHIP

更多
Horizontal gene transfer
Bioinformatics tools to detect horizontal gene transfer
pip install git(pip直接安装git上的项目)