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bioRxiv2016

Aequatus: An open-source homology browser

BackgroundPhylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as well as regions under positive or purifying selection within lineages. Gene family and orthogroup characterisation enables the identification of syntenic blocks, which can then be visualised with various tools. Unfortunately, currently available tools display only an overview of syntenic regions as a whole, limited to the gene level, and none provide further details about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes.\n\nFindingsWe present Aequatus, a standalone web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualisations. It relies on pre-calculated alignment and gene feature information typically held in, but not limited to, the Ensembl Compara and Core databases. We also offer Aequatus.js, a reusable JavaScript module that fulfils the visualisation aspects of Aequatus, available within the Galaxy web platform as a visualisation plugin, which can be used to visualise gene trees generated by the GeneSeqToFamily workflow.\n\nAvailabilityAequatus is an open-source tool freely available to download under the MIT license at https://github.com/TGAC/Aequatus. A demo server is available at http://aequatus.earlham.ac.uk/. A publicly available instance of the GeneSeqToFamily workflow to generate gene tree information and visualise it using Aequatus is available on the Galaxy EU server at https://usegalaxy.eu.\n\nContactsAnil.Thanki@earlham.ac.uk and Robert.Davey@earlham.ac.uk

Bioinformatics↗

bioRxiv2014

Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community.

Ash dieback is a fungal disease of ash trees caused by Hymenoscyphus pseudoalbidus that has swept across Europe in the last two decades and is a significant threat to the ash population. This emergent pathogen has been relatively poorly studied and little is known about its genetic make-up. In response to the arrival of this dangerous pathogen in the UK we took the unusual step of providing an open access database and initial sequence datasets to the scientific community for analysis prior to performing an analysis of our own. Our goal was to crowdsource genomic and other analyses and create a community analysing this pathogen. In this report on the evolution of the community and data and analysis obtained in the first year of this activity, we describe the nature and the volume of the contributions and reveal some preliminary insights into the genome and biology of H. pseudoalbidus that emerged. In particular our nascent community generated a first-pass genome assembly containing abundant collapsed AT-rich repeats indicating a typically complex genome structure. Our open science and crowdsourcing effort has brought a wealth of new knowledge about this emergent pathogen within a short time-frame. Our community endeavour highlights the positive impact that open, collaborative approaches can have on fast, responsive modern science.

Genomics↗