探索16S序列
一、准备数据和软件下载细菌全基因组序列NC_009648.1
https://www.ncbi.nlm.nih.gov/nuccore/NC_009648.1/?report=fasta 本地下载上传到服务器
mv sequence.fasta MGH78578.fasta 安装rnammer
官网https://link.zhihu.com/?target=https%3A//services.healthtech.dtu.dk/software.php
用edu邮箱申请下载地址
tar -zxf rnammer-1.2.src.tar.gz 下载并安装hmmer-2.3.2
wget http://eddylab.org/software/hmmer/hmmer-2.3.2.tar.gz
tar -zxf hmmer-2.3.2.tar.gz
cd hmmer-2.3.2/
./configure
make 更改rnnammer中两者的绝对路径
cd ..
vi rnammer 修改35行安装路径
/share/home/xiehs/biosoft/rnammer 修改50/53行安装路径
/share/home/xiehs/biosoft/rnammer/hmmer-2.3.2/src/hmmsearch 修改 core-rnammer脚本中2处cpu-1删去
<p>system sprintf('%s --cpu 1 --compat ...... and so on</p><p>改为system sprintf('%s --compat ...... and so on</p>
二、预测核糖体序列
报错：perl模块找不到，重新安装后，卸载原模块再安装
<p>#http://mirror.centos.org/centos/7/os/x86_64/Packages/找rpm</p><p>#https://zhuanlan.zhihu.com/p/352932647参考重装perl</p><p>#sudo rpm -e perl-constant-1.27-2.el7.noarch --nodeps 先卸载</p><p>#sudo rpm -ivh perl-constant-1.27-2.el7.noarch.rpm 再安装</p>#添加环境变量perl5lib
~/biosoft/rnammer/rnammer -S bac -m tsu,lsu,ssu -gff MGH78578.gff -f MGH78578.frn MGH78578.fasta
#统计结果
seqkit stat MGH78578.frn
#查看序列ID
grep "16s_rRNA" MGH78578.frn
#生成ID列表
grep "16s_rRNA" MGH78578.frn | awk'{print $1}' |sed -e 's/>//'>id.list
#提取16S序列
seqkit grep -r -f id.list MGH78578.frn >16S.fasta
#多序列比对
muscle -in 16S.fasta -out 16s.clw -clw
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