ANNOUNCING PFAM RELEASE 3.1
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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
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The Pfam consortium
98-09
