Posts Tagged ‘rfam’

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.

Submit your alignment to Rfam!

September 12, 2012

We’ve now made it easier for Rfam users to submit an alignment of a new family, or an improvement to an existing family in Rfam. As long as you have a Stockholm format alignment, you can use our web form to submit your alignment. Read the rest of this entry »

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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Rfam 11.0 is out!

August 14, 2012

The team behind Rfam is pleased to announce the release of Rfam 11.0. This release represents a major update from 10.1, primarily due to the upgrade of our underlying sequence database, Rfamseq.

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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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In Support of Wikipedia

January 17, 2012

Many of you will be aware of the proposed web blackout in response to the Stop Online Piracy Act which is currently going through the U.S. House of Representatives (you can read the BBC’s explanation of the Act here). If this Act is enforced, it has far-reaching consequences for the overall freedom of the internet. Editors of the English Wikipedia have taken the decision to close the English Wikipedia for 24 hours, starting at 0500 hrs on Wednesday 18th January. To respect this protest, we will also be making our Wikipedia content unavailable during this time.

You’ll still be able to access all the non-Wikipedia content – that is, all the covariance models and HMMs describing families, domain graphics, full and seed alignments, as well as our species trees.

Posted by Sarah and Alex

Rfam now available in UCSC Genome Browser, and other genome news.

November 2, 2011

We are pleased to announce the arrival of the Rfam Track Hub for the popular UCSC Genome browser. Rfam data has been available in the Ensembl browser for some time and provides links back to the Rfam annotation, and now this same functionality is available for the UCSC Genome Browser.

The hub file is available on our ftp site, and by following the instructions at the UCSC Genome Browser Custom Hub page, you can visualise Rfam annotations for the majority of species for which genomes are provided by the UCSC Genome Browser. Clicking on a match will give you exact start and stop positions, as well as links to the Rfam annotation page here at the Sanger. At the moment, bit scores or E-values for a given match aren’t yet available directly through the UCSC Genome Browser, though we’re working on it. Happy browsing!

Rfam types for Genome annotation

Xfam (in the forms of Sarah and Rob) attended the NIH Genome Annotation Workshop last week, and it was a great insight into the trials and tribulations of coming up with common standards that everyone’s happy with. It was also nice to hear that Rfam is being used exensively to annotate ncRNA features. However, there’s been some confusion amongst annotators when converting between Rfam types (such as CD-Box) and the ncRNA_classes required by INSDC under the ncRNA feature key. The ncRNA feature key is intended to describe non-coding RNAs that aren’t ribosomal or transfer RNAs; these use the rRNA and tRNA feature keys respectively.

To use the ncRNA feature key, annotators are required to supply an appropriate ncRNA_class, and this is where confusion arises, as there’s no perfect overlap between the Rfam entry types and the ncRNA classes. To reduce this, here at Rfam we’ve put together a handy translation guide to make it easy to know what ncRNA class you should apply if you are using an Rfam family to annotate a genome. There are also some cases where an INSDC type is more specific than the Rfam type; for example, we don’t have a specific telomerase RNA type, whereas there is a ncRNA_class called telomerase_RNA. Therefore any annotation to RF00025 can use the telomerase_RNA ncRNA_class category. You can find our table of Rfam types and their INSDC equivalents here.

You can also find out all you ever wanted to know about the feature tables used for genome annotation here, and here.