1、信号肽预测
下载软件signalp
SignalP - 5.0 - Services - DTU Health Techhttps://services.healthtech.dtu.dk/service.php?SignalP-5.0输入邮箱等注册信息(高校或科研机构邮箱),在邮箱里获取下载链接。
#下载软件
wget https://services.healthtech.dtu.dk/download/1d1d8c14-5304-4800-aafe-8e637b01a7c3/signalp-5.0b.Linux.tar.gz
#解压
tar zxf /home/u1342/software/signalp-5.0.Linux.tar.gz
#添加环境变量
echo 'PATH=$PATH:/opt/biosoft/signalp-5.0/bin' >> ~/.bashrc
#刷新环境变量
source ~/.bashrc
#运行
signalp -batch 30000 -org euk -fasta protein.fa -gff3 -mature
signalp命令参数:
-batch int
Number of sequences that the tool will run simultaneously. Decrease or increase size depending on your system memory. (default 10000)
-fasta string
Input file in fasta format.
-format string
Output format. 'long' for generating the predictions with plots, 'short' for the predictions without plots. (default "short")
-gff3
Make gff3 file of processed sequences.
-mature
Make fasta file with mature sequence.
-org string
Organism. Archaea: 'arch', Gram-positive: 'gram+', Gram-negative: 'gram-' or Eukarya: 'euk' (default "euk")
-plot string
Plots output format. When long output selected, choose between 'png', 'eps' or 'none' to get just a tabular file. (default "png")
-prefix string
Output files prefix. (default "Input file prefix")
-stdout
Write the prediction summary to the STDOUT.
-tmp string
Specify temporary file directory. (default "System default tmpdir")
-verbose
Verbose output. Specify '-verbose=false' to avoid printing. (default true)
-version
Prints version.
2、跨膜结构域预测
下载TMHMM,下载方法同上
#运行TMHMM,test.fa为上一步生成的mature.fa
tmhmm -noplot test.fa > tmhmm.txt
#提取没有跨膜结构域蛋白的ID,
grep 'Number of predicted TMHs: 0' tmhmm.txt > secreted_id.txt
#可使用sed命令删除 Number of predicted TMHs: 0,只留下ID编号
sed -i 's/Number of predicted TMHs: 0//g' secreted_id.txt
# 根据ID提取基因组分泌蛋白
seqkit grep -f secreted_id.txt protein.fa > secreted.fa
根据ID提取的蛋白序列即为基因组分泌蛋白