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The Pfam database of protein families and HMMs

Pfam 15.0 (August 2004, 7503 families)

Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families. Pfam version 15.0 (August 2004) contains alignments and models for 7503 protein families, based on the Swissprot 44.0 and SP-TrEMBL 27.0 protein sequence databases.

HELP	More information on Pfam, using this site, and the changes between Pfam releases.
PROTEIN SEARCH	Analyze a protein query sequence to find Pfam family matches.
DNA SEARCH	Analyze a DNA query sequence to find Pfam family matches. (Uses the GeneWise server at the Sanger Centre).
BROWSE PFAM	View Pfam annotation and alignments.
KEYWORD SEARCH	Query Pfam by keywords.
TAXONOMY SEARCH	Find Pfam families by taxonomy.
BROWSE SWISSPFAM	View the domain organization of a SWISSPROT/TrEMBL sequence according to Pfam.
PFAMALYZER	Explore Pfam via a Java-based interface, including extended domain query. (Links to Stockholm Pfam site).

FTP access to Pfam

Pfam alignments, HMMs, and other files are also available by FTP.

Most large files are compressed with GNU gzip, file extension .gz.

Browse the Pfam ftp site (St. Louis)
Release notes
Summary of changes from release 14.0 to 15.0, computer parsable
Pfam_ls - The PFAM HMM library, glocal alignment models.
Pfam_fs - The PFAM HMM library, local alignment models.
Pfam-A.full - The full alignments of the curated families.
Pfam-A.seed - The seed alignments of the curated families.
Pfam-B - PRODOM-generated alignments of sequence clusters in SWISSPROT and TrEMBL that are not modelled in the curated part of Pfam.
Pfam-C - Pfam Clans.
Swisspfam - The domain structure of SWISSPROT and TrEMBL proteins according to Pfam.
Swissother - Additional annotation of SWISSPROT and TrEMBL proteins.
domain.pnh - A pseudo-new hampshire format tree file of Pfam families and sequences.
St. Louis Pfam server - a portable package for mirroring the St. Louis Pfam Web site (for instance, behind a corporate firewall).
Copyright notice for Pfam.
The full text of the GNU Library General Public License that Pfam is licensed under.

Comments, questions, flames? Email <pfam@genetics.wustl.edu>.
Last modified: Thursday, 07-Oct-2004 13:13:21 CDT