Archive for the 'Releases' Category

Pfam 30.0 is available

July 1, 2016

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.



Structure of MMADHC dimer, PDB:5CV0


  • 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 (


Pfam 29.0 is now available

December 22, 2015

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 »

Meet Dfam2.0

October 30, 2015

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 ).

Read the rest of this entry »

Say hello to Dfam1.4

May 13, 2015

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.

Read the rest of this entry »

Dfam 1.3 released

January 7, 2015

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.

Read the rest of this entry »

Dfam 1.2 released

May 31, 2013

We are pleased to announce that we’ve released Dfam 1.2. This version represents a few important changes from 1.1, including increased sensitivity for many families, a new plot on the model page, and an improved Relationships tab.

Read the rest of this entry »

TreeFam 9 is now available!

May 3, 2013

We are happy to announce that TreeFam 9 is online and you can find it under

TreeFam 9 now has 109 species (vs. 79 in TreeFam 8) and is based on data from Ensembl v69, Ensembl Genomes v16, Wormbase and JGI.

This release marks an important step for TreeFam as it is the first release build since TreeFam has been resurrected.
Here is a list of the most important changes in TreeFam 9:

  • New website layout (adopting the Pfam/Rfam/Dfam layout)
  • Infrastructure move of web servers and databases to the EBI
  • Sequence search against the library of TreeFam family profiles
  • new tree visualisations in pure javascript using D3, e.g. see the BRCA2 gene tree here.
  • Pairwise homology download

We hope you find all the information you are looking for. If you don’t, please let us know so that we can include the information you want. The old website will remain online here.

If you have questions, suggestions or find bugs, don’t hesitate to contact us through our new forum here.

Happy treefamming,

the TreeFam team
(Fabian, Mateus)

Pfam 27.0 is now available!

March 22, 2013

In a blog post published just over a year ago, I proposed a number of changes to the content of Pfam to improve scalability and usability of the database.  These changes came into effect a few days ago, when we released Pfam 27.0.  This release of Pfam contains a total of 14831 families, with 1182 new families and 22 families killed since release 26.0. 80% of all proteins in UniProt contain a match to at least one Pfam domain, and 58% of all residues in the sequence database fall within a Pfam domain. Read the rest of this entry »

Dfam paper is an NAR “featured article”; RepeatMasker4 is out

January 12, 2013

We are pleased to announce that the Dfam paper (“Dfam: a database of repetitive DNA based on profile hidden Markov models“) is now available in the 2013 NAR Database issue, and has been selected as a “featured article” (meaning the NAR editorial board thinks it is among “the top 5% of papers in terms of originality, significance and scientific excellence”).

In other exciting news, two members of the Dfam consortium, Arian Smit and Robert Hubley (Institute for Systems Biology, Seattle), just released RepeatMasker 4.0. This is a major update that, among other important improvements, adds support for searching with Dfam and nhmmer. Go get yourself a copy at

Posted by Travis

Dfam 1.1 released

November 15, 2012

We are pleased to announce that we’ve released Dfam 1.1. This version represents a few important changes from 1.0, including updated hit results, a new tab for each entry page showing relationships to other entries, and improved handling of redundant profile hits.

Read the rest of this entry »