I would like to ask about the Pfam-A.hmm file. What is its role and function? From what I have researched, it serves as a core reference database consisting of Hidden Markov Models (HMMs) used in bioinformatics tools such as BiG-SCAPE. Could you explain which version of this file should be used and how it works in practice?
Welcome @Dinh_T_n_H_ng
You are correct! Pfam-A.hmm is a database of profile Hidden Markov Models (HMMs) representing curated protein families and domains from the Pfam database.
The file can be used with tools to search protein sequences for known domains and families.
Some Galaxy tools that use Pfam HMMs
| Galaxy tool | How it uses Pfam-A.hmm |
|---|---|
| PfamScan | Searches protein FASTA sequences against Pfam HMM profiles |
| HMMER hmmscan | Searches protein sequences against a profile HMM database |
| HMMER hmmfetch | Retrieves individual HMM profiles from a database |
| BiG-SCAPE | Uses Pfam HMM profiles to identify protein domains |
| InterProScan | Supports Pfam domain searches |
Galaxy Training Network (GTN) examples
Genome-wide alternative splicing analysis: Protein domain identification with PfamScan
Demonstrates using Pfam-A.hmm.gz, Pfam-A.hmm.dat.gz, and an optional active-sites file.
You can review the Help at the bottom of tool forms to learn more and to find links to tutorials that include the tool (if any). These are public tools, so you can find discussion and resources about them at most scientific forums, Biostars.org is one example!
References to explore
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InterPro – Pfam — Protein family and domain database.
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Pfam FTP documentation — Database files, descriptions, and download instructions.
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HMMER documentation — Tools for searching protein sequences against profile HMM databases.
BIG-SCAPE Help
See the bottom of the tool form for some tips about where to source reference data. The version you retrieve will be noted at the external data providers site!
Note: You can download Pfam-A.hmm.gz here and then unzip it or you can use the command: $ wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz && gunzip Pfam-A.hmm.gz in e.g. VSC.
Hope this helps you get oriented! 