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?
In November 2012, we announced that the Xfam groups were moving the few tens of metres from the Wellcome Trust Sanger Institute to the European Bioinformatics Institute. We warned you then, that the websites would also eventually move. Read the rest of this entry »
We’ve had a lot of questions from users recently, wondering why our pfam_scan.pl script doesn’t work with the latest release of the HMMER package, version 3.1b. This is a quick post to explain why that is, and what we’ve done about it. Read the rest of this entry »
The identification of orthologs in related organism is a routine task and many databases/tools are available to do that. Some of the databases can be installed locally, which is not ideal in cases where the target is to find orthologs for a single/few genes only. To fill this gap, we developed a quick orthology-on-the-fly prediction tool that is built on top of the HMMER search we introduced in release 9 and can be used here: www.treefam.org. Read the rest of this entry »
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.
Following on from Jaina and Marco’s blog post last week about conserved Human regions not in Pfam, I would like to give you some examples of how we have used the regions identified to improve existing Pfam families, and to create new ones. When available, we use three-dimensional structures to guide the boundary definitions of our families. In cases where there is no available structure, either for the protein in question or for other proteins in the same Pfam family, we base boundary decisions on sequence conservation. The following paragraphs give three examples of cases I have looked at recently.
Recently, we have been looking at how much of the human proteome is covered by Pfam (release 27.0), and ways in which we can improve this coverage. We have even written an open access paper about it that you can read here  that is part of the proceedings of the 2013 Biocuration conference. We used the human proteins in UniProtKB/Swiss-Prot  (~20,000 sequences) as our human proteome set, and found that while most of the sequences in this set have some Pfam annotation (90% have at least one Pfam domain), there is still much ground to cover before we have a complete map of all (conserved) human regions (HRs). Here, rather than repeating what we presented in the paper (did we mention it is open access? :-)), we would like to tell you more about the impact this study is having on our strategies for selecting target regions to be added to Pfam.