Search Pfam with Hmmer

1. install HMMer

2. from ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/ download pfam database Pfam-A.hmm

3.  obtain PFAM Database HMM file . HMM Files are text files , It needs to be converted into binary format , To speed up the operation , Compress at the same time , And build an index database . command ：

hmmpress Pfam-A.hmm 

3. Use hmmscan Conduct Pfam Note example ：

hmmscan -o out.txt --tblout out.tbl --noali -E 1e-5 Pfam-A.hmm file.fasta

（ Thank you, Mr. Chen Lian, for your letter blog http://www.chenlianfu.com/?p=2274, This article is just a record of learning from his blog ）

attach  hmmscan [-options] The meaning of several main options

-h Display help information

-o FILE Output the results to the specified file . The default is output to standard output .

--tblout FILE Output the results of the protein family in tabular form to the specified file . By default, this file is not output .

--domtblout FILE Output the comparison results of protein domains in tabular form to the specified file . By default, this file is not output . This table contains query The matching information between the start and end sites of the sequence and the start and end sites of the target sequence .

--acc Include PF The number of , The default is the name of the protein family .

--noali The output result does not contain comparison information . The size of the output file will be smaller . -E FLOAT default:10.0 Set up E_value threshold , Recommended setting as 1e-5 .

-T FLOAT Set up Score threshold . --domE FLOAT default:10.0 Set up E_value threshold . The parameters and -E The parameters are similar to , But is domain Compare the set value .