Pfam 2.1 - Protein families database of alignments and HMMs

Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.

Pfam's alignments are of complete domains, not of motif signatures. Pfam's development is tightly tied to the development of hidden Markov model (HMM) profile methods of modeling protein multiple alignments. Our goal is to enable rapid automatic annotation of common protein domains.

Pfam - consortium including researchers at the Sanger Centre in Hinxton UK, the WashU Dept. of Genetics in St. Louis USA, and Erik Sonnhammer, now at the NCBI.

Pfam is freely distributed under the terms of the GNU Library General Public License.

Interactive WWW access to Pfam

You can search your favorite sequence against Pfam; access, view, and download individual alignments from Pfam; or download HMMs that you can use locally if you have installed HMMER hidden Markov model software. Output pages are hyperlinked to other relevant databases, including Swissprot, Genbank, PDB, PROSITE, and Medline.

Search Pfam. Search your sequence for matches to Pfam protein domain models.
Browse Pfam. View or download one or more of the current alignments.
Browse "SwissPfam". View the domain organisation of any Swissprot sequence according to Pfam, based on the results of a precomputed Pfam HMM analysis.

FTP files

Full alignments of 527 curated Pfam families.
Seed alignments of 527 curated Pfam families.
HMM library -- The PFAM HMM library. 527 models.
Swiss-Pfam -- the domain structure of SwissProt release 34, according to Pfam.

Comments or questions? Send email to <pfam@genetics.wustl.edu>.