pfam的使用-自用
首先,这篇文章是引用的https://www.jianshu.com/p/fb3bd3de1c38这篇文章的
其中有一些步骤我没有做过,保存在来步骤:
数据库下载
wget ftp://ftp.ebi.ac.uk:21/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
wget ftp://ftp.ebi.ac.uk:21/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz
wget ftp://ftp.ebi.ac.uk:21/pub/databases/Pfam/current_release/active_site.dat.gz
gunzip *.gz
然后建库:
$ hmmpress Pfam-A.hmm
建库之后是这个样子的:
[zhangzhd@vm-login02 pfam]$ hmmpress Pfam-A.hmm
Working... done.
Pressed and indexed 19632 HMMs (19632 names and 19632 accessions).
Models pressed into binary file: Pfam-A.hmm.h3m
SSI index for binary model file: Pfam-A.hmm.h3i
Profiles (MSV part) pressed into: Pfam-A.hmm.h3f
Profiles (remainder) pressed into: Pfam-A.hmm.h3p
然后就可以根据这个来进行是使用了:
pfam_scan.pl -fasta /public/home/TonyWuLab/zhangzhd/hmmer/onesequence.fasta -dir /public/home/TonyWuLab/zhangzhd/pfam/ -outfile testresult -as
这个地方注意一下:-dir是路径不是文件