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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 7.0 contains 3360 families. 69% of proteins in SWISSPROT 40 and TrEMBL 18 have at least one match to a Pfam family.
For interactive access and searching see URLs
http://www.sanger.ac.uk/Software/Pfam
http://pfam.wustl.edu
http://www.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/
ftp://ftp.cgr.ki.se/pub/data/Pfam/
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