Pfam::Home

Pfam::Home

Interactive WWW access to Pfam

• TEXT SEARCH - Query Pfam by keywords.

• PROTEIN HMM SEARCH - Find Pfam domain matches in your protein sequence.

• DNA HMM SEARCH - Find Pfam domain matches in your DNA sequence.

• BROWSE PFAM - View Pfam annotation and alignments.

• BROWSE SWISSPFAM - View the domain organisation of any SWISSPROT/TrEMBL sequence according to Pfam.

• NIFAS - Analyze the evolution of domain combinations with NIFAS.

• DOMAIN QUERY - Query Pfam by domain architecture.

• Pfam::Alyzer - Graphical user-friendly interface to Pfam. It contains most of the functionalities of the tools above and features an extended domain query based on an intuitive graphical query language.

• Advanced options: Alignment retrieval with options

• More information and help on Pfam

• Pfam mirror servers worldwide: WashU (USA), Sanger (UK), INRA (France), CCBB (Korea)

FTP access to Pfam

• Hyperlink directly to the ftp site
• Release notes Pfam_format
• Pfam_ls - The Pfam global-local (ls) HMM library.
• Pfam_fs - The Pfam local-local (fs) HMM library.
• Pfam-A.full - The full alignments of the curated families.
• Pfam-A.seed - The seed alignments of the curated families.
• Pfam-B - Low-quality automatically generated alignments of sequence clusters in SWISSPROT and TrEMBL that are not modelled in the curated part of Pfam.
• Pfam-C - Pfam Clans
• swisspfam - The domain structure of SWISSPROT and TrEMBL proteins according to Pfam.
• pfamseq - The raw sequences from SWISSPROT and TrEMBL that Pfam is based upon.
• prior.tar - A set of prior files for specific Pfam families.
• diff - Differences relative to the previous release.
• Copyright notice for Pfam.
• The full text of the GNU Library General Public License that Pfam is licensed under.