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Once we design a probe set, we follow sequence capture protocols to enrich DNA libraries for the target UCEs, usually in multiplex. Faircloth BC, Mc Cormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC. Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales. These talks should give a general idea of where we're going with new research projects that use UCEs.
Following enrichment, we sequence the DNA enriched for UCEs using massively parallel sequencing. Crawford NG, Faircloth BC, Mc Cormack JE, Brumfield RT, Winker K, Glenn TC. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Go to talks » Below are several commercial laboratories offering UCE enrichment as a service.
MYcroarray has even made a discounted "pilot" sized kit available for labs who want to do some test enrichments.
Order enrichment kits from MYcroarray » The linked FASTA file (ZIP archive) contains probe sequences (120 nt) designed for synthesis as part of a Agilent Sure Select or Mycro Array My Bait target enrichment kit.
We used these probes for our analysis of early diverging teleosts.
By their deposition in Dryad, all probes are available under a CC0 license, thus freely available for you to use, without restriction.
Concatenates reads into an "interleaved" file for use with velvet.
Report an issue with illumiprocessor Get illumiprocessor » A program started by Nick Crawford with contributions from Brant Faircloth for parallel computation of individual genetrees and the estimation of a species tree from gene tree data.
Because UCEs are conserved across disparate taxa, UCEs are also That's an extremely good question, and one to which we do not entirely know the answer (Dermitzakis et al. UCEs have been associated with gene regulation (Pennachio et al. However, gene knockouts of UCE loci in mice resulted in viable, fertile offspring (Ahituv et al.Allows analysis and bootstrapping of large datasets.Uses elastic map reduce or multiprocessing to analyze data in parallel. As their name implies, ultraconserved elements (UCEs) are highly conserved regions of organismal genomes shared among evolutionary distant taxa - for instance, birds share many UCEs with humans.UCEs were first described in a wonderful manuscript by Gil Bejerano et al.