Pfam 3.1 release

Alex Bateman agb at
Thu Sep 17 04:59:20 EST 1998

                ANNOUNCING PFAM RELEASE 3.1

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 3.1 contains 1313 families.  55% of proteins in SWISSPROT 35
and TrEMBL 5 have at least one match to a Pfam family.

The release of Pfam 3.1 has many changes from the 2.1 release.
In summary the main changes are:

         786 new families have been added.
         Sequence searching and alignment use the new HMMER2 software.
         It is now built on a "complete" protein database including
         translations from Genbank/EMBL (SWISSPROT 35 plus SPTrEMBL 5).

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

The Pfam Web site can be set up locally from a single tar file
available at

The Pfam consortium

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