Pfam 3.1 release

Alex Bateman agb at sanger.ac.uk
Tue Sep 22 21:49:23 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

               http://www.sanger.ac.uk/Software/Pfam/
               http://pfam.wustl.edu/

The release is also available in flat file by anonymous ftp:

               ftp://ftp.sanger.ac.uk/pub/databases/Pfam/
               ftp://ftp.genetics.wustl.edu/pub/Pfam/

The Pfam HMM library is compatible with HMMER2 software, available
from
	       http://hmmer.wustl.edu/

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

	       ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Web



___________________
The Pfam consortium
98-09





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