Repetitive elements in vertebrate genomes

Updated 2015 February 8th to include some scatter plots of genome size versus repeat content.

I was writing about the make up of genomes today and was looking up statistics on repetitive elements in vertebrate genomes. While I could find individual papers with repetitive element statistics for a particular genome, I was unable to find a summary for a list of vertebrate genomes (but to be honest I didn't look very hard). So I thought I'll make my own and share it on my blog and via figshare. I will use the RepeatMasker annotations provided via the UCSC genome browser.

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Genomic Regions Enrichment of Annotations Tool

The Genomic Regions Enrichment of Annotations Tool (GREAT) is a tool that allows you to find enriched ontological terms in a set of genomic regions. This talk (running time ~1 hour) gives an overview of the tool. In brief, GREAT is an alternative to gene-centric enrichment tools such as DAVID and uses a binomial test to test for ontology enrichment. Figure 1b in the GREAT paper explains how GREAT models functional annotations in the genome. The advantage of using a binomial model, is that it takes into account the probability of having a genomic region overlap a region associated with a particular ontology, so that ontologies that are biased in terms of genome coverage are taken into account. GREAT incorporates annotations from 20 ontologies and is available as a web application. As stated in the paper, the utility of GREAT is not limited to just ChIP-seq data and for those who are more interested, check out their paper.

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Rett syndrome and piRNAs

Two years ago we were invited to write an article in a Special Issue of the Disease Markers journal, which was dedicated to autism spectrum disorders (ASD) and biomarkers. From Wikipedia, ASD are

disorders characterised by social deficits and communication difficulties, stereotyped or repetitive behaviours and interests, and in some cases, cognitive delays.

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