Using tools from Ash Tree Genomes

BLAST searches of ash genomes

Here, we have made available for searching our current genome assemblies of Fraxinus.

The assemblies with names beginning "BATG" are of the UK reference Fraxinus excelsior tree and have been published in this paper:

Elizabeth S. A. Sollars, Andrea L. Harper, Laura J. Kelly, Christine M. Sambles, Ricardo H. Ramirez-Gonzalez, David Swarbreck, Gemy Kaithakottil, Endymion D. Cooper, Cristobal Uauy, Lenka Havlickova, Gemma Worswick, David J. Studholme, Jasmin Zohren, Deborah L. Salmon, Bernardo J. Clavijo, Yi Li, Zhesi He, Alison Fellgett, Lea Vig McKinney, Lene Rostgaard Nielsen, Gerry C. Douglas, Erik Dahl Kjær, J. Allan Downie, David Boshier, Steve Lee, Jo Clark, Murray Grant, Ian Bancroft, Mario Caccamo and Richard J. A. Buggs (2016) Genome sequence and genetic diversity of European ash trees. Nature doi:10.1038/nature20786

Please cite this paper if you use the "BATG" assemblies.

We have also made available to BLAST preliminary genome assemblies of other Fraxinus species, assembled by Laura Kelly and Endymion Cooper. These data are as yet unpublished. If you want to publish any analysis of these data you must either wait until we have published them in a journal, or contact Richard Buggs to negotiate a co-authored paper.

As a public service, preliminary sequences of these genomes are being made available before scientific publication. The purpose of this policy is to balance the desire that the ash genomes be made available to the scientific community working on ash dieback and emerald ash borer as soon as possible with the reasonable expectation that the group responsible for the sequencing will publish their results in peer reviewed journals without concerns about potential pre-emption by other groups that did not directly participate in the effort.

These pre-publication data are preliminary and may contain errors. The goal of our policy is that early release should enable the progress of science. By accessing these data, you agree not to submit to scientific journals any articles containing analyses of these data data prior to peer-reviewed journal publication by us and our collaborators of a comprehensive genome analysis.

Any analyses involving data are included in this data usage policy, including annotation of genes, identification of sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, etc., and whole-genome comparisons of regions of among-species conservation. Also included are uses of the genome data as a reference for transcriptomic analyses (RNA seq, bisulfite seq, chip seq or similar). Interested parties are encouraged to contact the the principal investigator if they wish to discuss the possibility of collaborative publication of such analyses.

The data may be freely downloaded and used by all who respect the restrictions in the previous paragraphs. In the period before the peer-reviewed journal publication by BATG, the assembly and raw sequence reads should not be redistributed or repackaged without permission from the British Ash Tree Genome Project principal investigator. Any agreed redistribution of the data during this period should carry this notice: "The British Ash Tree Genome Project provides these data in good faith, but makes no warranty, expressed or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used."

Once moved to unreserved status, the data will be freely available for any subsequent use.

We have also made the "Tree 35" Fraxinus excelsior genome assembly from the OpenAshDieback website available for BLAST searches here. Please refer to the oadb website for details and terms of use of this data.

By accessing this tool you are agreeing to the terms outlined above.

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Note on previously available BLAST databases for other Fraxinus species: We previously made available to BLAST preliminary consensus sequences of the genomes of other ash species, generated from mappings to the Fraxinus excelsior reference (assembly BATG0.5) conducted by Laura Kelly. We have now (as of 16.03.17) removed these databases as we are replacing them with de novo genome assemblies for the same individuals. If you want further information on the previously available BLAST databases (those which followed the naming format “Species_name_v1” and “Species_name_v2”) please contact Richard Buggs.