ITEP-microbial pan-genomes工具

ITEP: An integrated toolkit for exploration of microbial pan-genomes

一、ITEP 安装

没有git的先安装git：

sudo apt-get install git

下载ITEP：

git clone git@github.com:mattb112885/clusterDbAnalysis

Verifying permissions：

cd clusterDbAnalysis

sudo chmod u+x src/*.py

sudo chmod u+x src/*.sh

sudo chmod u+x src/internal/*.py

sudo chmod u+x src/internal/*.sh

sudo chmod u+x src/utilities/*.py

sudo chmod u+x src/utilities/*.sh

sudo chmod u+x scripts/*.py

sudo chmod u+x scripts/*.sh

设置环境变量：

vim ~/.bashrc

i

source $HOME/tools/ITEP/clusterDbAnalysis/SourceMe.sh#具体按照自己的目录来写

按ESC键

shift + :

wq!

source ~/.bashrc

依赖包检查：

进入软件目录，运行检查命令，会列出未安装的依赖包，然后依次安装即可：

cd clusterDbAnalysis

./checkForDependencies.sh

比较难安装的依赖包：

install libdb4.8++-dev

sudo add-apt-repository ppa:bitcoin/bitcoin

sudo apt-get update

sudo apt-get install -y libdb4.8-dev libdb4.8++-dev

libwxbase2.8-0

sudo dpkg -i libwxbase2.8-0_2.8.12.1+dfsg2-2ubuntu2+1_webupd8_xenial0_amd64.deb

libpng12-0

sudo dpkg -i libpng12-0_1.2.54-1ubuntu1_amd64.deb

libwxgtk2.8-0

sudo dpkg -i libwxgtk2.8-0_2.8.12.1+dfsg2-2ubuntu2+1_webupd8_xenial0_amd64.deb

myrast

sudo dpkg -i myrast-runtime_1.0-1ubuntu1_amd64.deb

sudo dpkg -i myrast_33-1ubuntu2_amd64.deb

二、使用

1. 运行前首先要在软件目录下运行如下命令：

source SourceMe.sh

2. 导入数据

需要genebank格式的文件

3. 指定要进行cluster的基因组列表

4. 建立ITEP数据库

建立数据库1-BLASTP and BLASTN

建立数据库2-MCL Clustering

建立数据库2-将来自其他cluster方法的结果导入ITEP

建立数据库3-Contig import

建立数据库4-RPSBLAST

5. 比较基因组分析

（1）Entry points into the database (read this first!)

（2）Searching for genes by gene properties

（3）Searching for genes by homology with other genes

（4）Obtaining information about genes

（5）Obtaining the complete sequences of contigs, genes or proteins

（6）Extracting DNA and amino acid sequences from a region of a genome, gene or protein

（7）Building alignments and trees

（8）Analyzing gene neighborhoods

（9）Searching for gene families by presence and absence patterns

（10）Visualizing homology patterns

（11）Building a concatinated gene tree

（12）Generating draft metabolic reconstructions from a reference

（13）Searching for missing genes and identifying causes for absence with tBLASTn

（14）Identifying the upstream regions of homologous proteins

（15）Searching for functions using conserved domains

（16）Adding user-defined gene data to ITEP

（17）Obtaining a list of bidirectional-best BLAST hits

（18）Turning ITEP IDs into human-readable formats

（19）Comparing the results of different clustering approaches

（20）Using the Graphical User Interface