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 »
The latest TreeFam release 9 has 15,736 gene families. These families vary significantly in size (number of family members), conservation (alignment conservation) and taxonomic diversity (younger families that are only found in e.g. Vertebrates vs. older ones that were present in the last common ancestor of Metazoa).
Visualising & exploring gene families
We have always wanted to find a way to visualise our families according to the above mentioned criteria.
Wouldn’t it be nice if you could easily see all highly conserved families or all families with >= 400 genes? Read the rest of this entry »
We have just advertised a 9-month maternity cover position in Pfam. We are looking for a skilled Bioinformatician to help us take Pfam into its next phase of development as we become more integrated into the European Bioinformatics Institute (EMBL-EBI).
Essential knowledge, skills and experience:
- Degree in Science with relevant experience
- Computer literacy (unix experience)
- Programming skills in Perl, including OO Perl
- Familiarity with writing production software
- MySQL, or similar, expertise
- Experience working with biological sequence data
- Good communications skills
See all the details on the EBI jobs page.
Rfam is recruiting! We are currently recruiting an RNA informatician to join our team. We’re looking for someone really enthusiastic about RNA and who’s interested in working with Rfam as we move to genome-based alignments and explore new technologies for the database and website.
If this is you, why not apply to join us as a Senior Bioinformatician?