Posts Tagged ‘pfam’

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 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.

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What’s new in AntiFam?

November 13, 2012

We have recently produced a new release of AntiFam, release 3.0. AntiFam has grown in size, and release 3.0 contains 54 entries – compared to just 23 when we last blogged about AntiFam (release 1.1).  Over 80 % of these new entries arise from translations of non-coding RNAs, including several families from translations of rRNA, tmRNA and RNaseP.

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We’re on the move

November 1, 2012

After 15 great years at the Sanger Institute we are on the move. On the 1st November, the Cambridge Xfam group will be taking up residence at the European Bioinformatics Institute on the other side of the Wellcome Trust Genome Campus. We’ll keep running the websites at Sanger for a bit longer, but eventually we’ll get them migrated over to EBI webspace. We’re hoping that the move will not cause any disruption to our users, but we might be a little bit slower at responding to your questions and bug reports.
We’ll keep you posted on updates to the website and database locations using the blog and our Twitter account.

Dfam: A database of repetitive DNA elements

September 6, 2012

We are pleased to introduce Dfam 1.0, a database of profile HMMs for repetitive DNA elements. Repetitive DNA, especially the remnants of transposable elements, makes up a large fraction of many genomes, especially eukaryotic. Accurate annotation of these TEs both simplifies downstream genomic analysis and enables research into their fascinating biology and impact on the genome.

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Getting all Pfam-A domains for a proteome

June 21, 2012

We’ve had a few helpdesk tickets in the last few months asking how to download all of the Pfam-A domains for a particular species. This information can be quite difficult to obtain: getting it requires either downloading and installing a sub-set of the tables in our MySQL database, or else searching all of the sequences from the species of interest against Pfam, probably using our batch search.

We thought it would be useful to simplify the process and add the domain information directly to our proteome pages, so we’ve just done exactly that. Read the rest of this entry »

Does my family of interest have a determined 3D protein structure?

May 9, 2012

Two related questions that we are often asked via the Pfam helpdesk is ‘Which families have a known three-dimensional structure?’ and ‘Why is a particular a PDB structure not found in Pfam’.  You may think that there are obvious answers to these questions – but as with many things in life the answer is not necessarily as straight forward as you would have thought. In this joint posting between Andreas Prlic (senior scientist at RCSB Protein Data Bank) and myself (Rob Finn, Pfam Production Lead), we will elaborate on the way the PDB and Pfam cross referencing occurs, why discrepancies occurred in the past and describe the pipeline that the RCSB PDB has implemented using the HMMER web services API, which should provide the most current answer to these  questions. Read the rest of this entry »

TreeFam is back with a new release !

March 27, 2012

As some of you will already be aware, the Xfam family has recently gained a new member: the TreeFam database.
TreeFam aims to provide phylogenetic trees and orthology predictions for all animal genes.

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Introducing AntiFam

March 21, 2012

AntiFam [1] is the newest addition to the Xfam brand. It is a database of hidden Markov models (HMMs) designed to identify spurious open reading frames (ORFs). It is available now on our ftp site:
ftp://ftp.sanger.ac.uk/pub/databases/Pfam/AntiFam/

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Proposed Pfam release changes

February 27, 2012

The current Pfam release, version 26.0, took approximately 4 months to nurse through the various stages of updating the sequence database, resolving overlaps between families, rebuilding the MySQL database and performing all of the post-processing that constitutes the ‘release’.  The production team strives to make two releases a year, but I really do not fancy spend two thirds of a year on Pfam releases.  Thus, with my colleagues, I have been reviewing what we do and why we do it and, probably more importantly, assessing how much different sections of the Web site are used.  Below is a list of changes that are going to happen in the next release, release 27.0.

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