What Pfam did in 2008

I thought it would be useful to give a quick overview of some of the major things that have been going on behind the scenes at Pfam during 2008. Overall it may have seemed like a quiet year for our users as we only made one public release of data in July, release 23.0. However, like a paddling duck, the calmness viewed from above belies some furious paddling below.

Early adoption of HMMER3

As the first post suggested, this blog will partly describe the progress and issues faced with the migration of Pfam to HMMER3.  We’ve been waiting for the mercurial HMMER3 for well over a year now, watching all the while its ever receding release date.  However, it has finally been released, albeit in alpha phase! Given Sean Eddy’s past record on HMMER2, particularly his attention to detail and his hatred of bugs in his software, we (Pfam) are already confident enough to be looking at migrating to HMMER3. This post will set out the rationale for moving Pfam to HMMER3 quickly and look at some of the issues that will inevitably follow such a move.

Rfam release 9.1

Rfam version 9.1 was released on 12^th January 2009. This release included 1372 familes – a big increase from release 9.0, which contained 603 families. The underlying sequence database was based on EMBL 92.

Welcome to the Xfam blog

Welcome to the new blog for the Xfam databases ! Xfam is our shorthand for the combination of Pfam and Rfam databases, which we note will also future-proof us, in case we add any further databases to the brand.

We hope that this blog will become a useful point of reference, where our users can learn about what is going on behind the scenes at Xfam central. We will be announcing some important changes that are coming with the eagerly awaited release of HMMER 3. As well as announcing new releases of the data and website, we’ll also try to discuss our philosophy on protein/RNA domains and sequence classification. If there are other topics that you would like to hear more about, why not leave us a comment.