We now have an online Quick Tour that provides a brief introduction to the Pfam protein families database. It provides a basic description of Pfam, as well as advice on how to search the database and discover protein-related information. The tour also showcases various tools that allow users to visualize data in Pfam, and explains where to find out more about the resource. We recommend taking the tour to learn how to use Pfam effectively.
Pfam 30.0, our second release based on UniProt reference proteomes, is now available. The new release contains a total of 16,306 families, with 22 new families and 11 families killed since the last release. The UniProt reference proteome set has expanded and now includes 17.7 million sequences, compared with 11.9 million when we made Pfam 29.0. In this release, we have updated the annotations on hundreds of Pfam entries, and renamed some of our Domains of Unknown Function (DUF) families.
DUFs are protein domains whose function is uncharacterised. Over time, as scientific knowledge increases and new data about proteins comes to light, more information about the function of a domain may become available. As a result, DUFs can be renamed and re-annotated with more meaningful descriptions. As part of Pfam 30.0, we have re-annotated 116 DUFs based on updated information in the UniProtKB database, the scientific literature, and feedback from Pfam and InterPro users. Examples of some our DUF updates in Pfam 30.0 are given below:
- PF10265, created in release 23.0 and originally named DUF2217, has been renamed to Miga, a family of proteins that promote mitochondrial fusion.
- PF10229, created in release 23.0 and originally named DUF2246, has been renamed as MMADHC, as it represents methylmalonic aciduria and homocystinuria type D proteins and their homologues. The structure of this domain is shown below.
- PF12822, created in release 25.0 and originally named DUF3816, has been renamed to ECF_trnsprt, since it contains proteins identified as the substrate-specific component of energy-coupling factor (ECF) transporters.
Please note that we may change the identifier for a family (e.g. DUF2217), but we never change the accession for a family (e.g. PF10265).
If you find any more DUFs that can be assigned a name based on function, or any other annotation updates, please get in touch with us (email@example.com).
We are happy to announce a new release of Rfam. Version 12.1, based on the same sequence dataset as Rfam 12.0, features over 20 new families, a new clan competing algorithm, a publicly accessible MySQL database, and many website fixes.
Pfam 29.0, our second release of 2015, contains 16295 entries and 559 clans. We have made some major changes to our underlying sequence database and the data that are displayed on the website, which we’ve outlined below. Full details can be found in our Nucleic Acids Research paper, which is available here. Read the rest of this entry »
Dfam is growing up. This is the first major expansion of the database since it’s inception. We’ve added repeat families from four new organisms: mouse, zebrafish, fruit fly, and nematode. In total, this release includes 2,844 new familes ( 4,150 total ).
We are pleased to announce the return of the Rfam Track Hub for the UCSC Genome Browser. This hub is available on our ftp site. The hub prodives annotation for the most recent assemblies eight different species at present: Human (hg38), Mouse (mm10), C.elegans (ce10), Chicken (galGal4), C. intestinalis (ci2), Zebrafish (danRer7), Drosophila (dm6) and S. cerevisiae (sacCer3).
With Dfam, we are striving to build models of repeat families that yield high sensitivity without undue false annotation. In this release of Dfam, we have improved our model building strategy to reduce the potential for false annotation, especially in the context of overextending alignments around true interspersed repeat instances.
We are pleased to announce the release of Dfam 1.3. This release includes almost 200 new repeat families and updates the underlying human genome to hg38.
We are pleased to announce the release of Rfam 12.0! Read the rest of this entry »
Back in November 2012 we announced that the Xfam team in the UK was moving from the Wellcome Trust Sanger Institute to the European Bioinformatics Institute (EMBL-EBI), just next door on the Wellcome Trust Genome Campus. On Tuesday we completed that move by switching off the Pfam and Rfam websites inside Sanger and redirecting all traffic to our shiny new home at xfam.org. You can now find the Pfam and Rfam websites at pfam.xfam.org and rfam.xfam.org respectively. Read the rest of this entry »