IUBio

ANNOUNCING PFAM RELEASE 4.0

Kevin Howe klh at sanger.ac.uk
Fri May 21 07:42:59 EST 1999


                ANNOUNCING PFAM RELEASE 4.0
                ===========================


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/

___________________
The Pfam consortium
99-05






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