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 »
Archive for the 'TreeFam' Category
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 »
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 happy to announce that TreeFam 9 is online and you can find it under http://www.treefam.org.
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
- 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.
the TreeFam team
Behind the scenes we are working hard on building the next TreeFam release, which will be TreeFam 9.
TreeFam 9 will have 109 species, that is a 37% increase over TreeFam 8. Most of the species come from EnsEMBL (v.69) and EnsEMBL genomes (v.16) with a few ones coming from JGI.
Besides that – and probably most important for the user – will be our new web site. Based on the success of other Xfam-databases like Pfam , Rfam  and -most recently- Dfam , we decided to give the TreeFam website a face lift by adapting it to the Xfam look&feel.
So, there are great things to come and soon we will have our next blog post.
The next TreeFam blog post will then be about TreeFam 9!