The BioInformer nr. 4, 1998 --- Pfam 3.1




	A publication of EMBL - Outstation Hinxton, The European Bioinformatics Institute


		Pfam 3.1 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. This release 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). Availability Pfam 3.1 is available on the web, offering access to multiple sequence alignments and profile HMM searches. Information by: Ewan Birney Resources and further information The Sanger Centre http://www.sanger.ac.uk/ Pfam homepage (UK) http://www.sanger.ac.uk/Software/Pfam/ Pfam flat file database ftp site ftp://ftp.sanger.ac.uk/pub/databases/Pfam/ Pfam downloadable web pages - Pfam web site can be set up locally from a single tar file ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Web/ Washington University http://www.wustl.edu/ Genetics Department http://www.genetics.wustl.edu/ Pfam homepage (USA) http://pfam.wustl.edu/ Pfam flat file database ftp site ftp://ftp.genetics.wustl.edu/pub/Pfam/ HMMER2 software - Pfam HMM library is compatible with this sofwtare http://hmmer.wustl.edu/ External sites are not endorsed by EMBL-EBI

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