I: Download and install
The latest version of the Pfam database no longer has Pfam-B, so you can download Pfam-A.hmm, Pfam-A.hmm.dat and active_site.dat directly, and then unzip the downloaded files: gunzip Pfam-A.hmm.gz Pfam-A.hmm.dat.gz active_site .dat.gz
II: Formatting the Pfam database via hmmerspress
$hmmpress Pfam-A.hmm
III: Running the program
nohup pfam_scan.pl -fasta /your_path/masp.protein.fasta -dir /your_path/PfamScan/Pfam_data -outfile masp_pfam -cpu 16 &IV: Format of results
The results of pfamscan protein structural domain partially analyzed are described as follows.
(1) seq_id: transcript ID + [0,1,2], transcripts not present in the list are noncoding
(2) hmm start: the start position of the structural domain to be compared.
(3) hmm end: comparison to the end position of the structural field
(4) hmm acc: the ID of the structural domain of pfam.
(5) hmm name: name of the pfam structure domain
(6) hmm length: the length of the pfam structure field.
(7) bit score: the score of the pfam structure domain
(8) E-value: the E-value of the comparison, the condition of pfam structure domain filtering is: Evalue < 0.001
