ANNOUNCING PFAM RELEASE 4.0
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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 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
discussed below.
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
http://www.sanger.ac.uk/Software/Pfam/http://pfam.wustl.edu/http://kisac.cgr.ki.se/Pfam/
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/
and also the Wise2 software, available from
http://www.sanger.ac.uk/Software/Wise2/
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The Pfam consortium
99-05
