ANNOUNCING PFAM RELEASE 4.0
Pfam is a collection of protein domain family alignments which were
constructed semi-automatically using profile hidden Markov models.
Pfam families contain functional annotation and cross-references to
other databases. Query sequences can be searched against the Pfam
library of profile hidden Markov models at the web sites below.
Pfam 4.0 contains 1465 families. 57% of proteins in SWISSPROT 37
and TrEMBL 9 have at least one match to a Pfam family.
The changes between Pfam release 3.4 and Pfam release 4.0 are
Pfam-B the automatically generated part of Pfam is now constructed
from Prodom release 99.1. Regions that are already in a curated
Pfam family are removed and Prodom alignments are split based on
Pfam domain boundaries.
For interactive access and searching see URLs
The release is also available in flat file by anonymous ftp:
The Pfam HMM library is compatible with HMMER2 software, available
and also the Wise2 software, available from
The Pfam consortium