Archive for the 'Dfam' Category

Introducing Dfam_consensus – Dfam’s consensus sequence twin

May 18, 2017

Since its inception in 2012, Dfam has demonstrated the promise of using profile hidden Markov Models (HMMs) to improve the detection sensitivity and annotation quality of Transposable Element (TEs) families in human[1] and subsequently for four additional reference organisms[2].  Despite these advances, the tools used to discover new families ( de-novo repeat finders ), improve families ( extend, defragment, subfamily clustering ), and classify TE families continue to depend on consensus sequence models.  This discordance between methodologies is a direct impediment to Dfam’s expansion.

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Meet Dfam2.0

October 30, 2015

Dfam is growing up. This is the first major expansion of the database since it’s inception. We’ve added repeat families from four new organisms: mouse, zebrafish, fruit fly, and nematode. In total, this release includes 2,844 new familes ( 4,150 total ).

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Say hello to Dfam1.4

May 13, 2015

With Dfam, we are striving to build models of repeat families that yield high sensitivity without undue false annotation.  In this release of Dfam, we have improved our model building strategy to reduce the potential for false annotation, especially in the context of overextending alignments around true interspersed repeat instances.

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Dfam 1.3 released

January 7, 2015

We are pleased to announce the release of Dfam 1.3. This release includes almost 200 new repeat families and updates the underlying human genome to hg38.

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We’ve moved, now the websites

January 30, 2014

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 »

Dfam 1.2 released

May 31, 2013

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.

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Dfam paper is an NAR “featured article”; RepeatMasker4 is out

January 12, 2013

We are pleased to announce that the Dfam paper (“Dfam: a database of repetitive DNA based on profile hidden Markov models“) is now available in the 2013 NAR Database issue, and has been selected as a “featured article” (meaning the NAR editorial board thinks it is among “the top 5% of papers in terms of originality, significance and scientific excellence”).

In other exciting news, two members of the Dfam consortium, Arian Smit and Robert Hubley (Institute for Systems Biology, Seattle), just released RepeatMasker 4.0. This is a major update that, among other important improvements, adds support for searching with Dfam and nhmmer. Go get yourself a copy at http://www.repeatmasker.org/

Posted by Travis

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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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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