BBSRC-NSF/BIO: Next generation collaborative annotation of genomes and synteny

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Development of the genome annotation tools Artemis and Apollo has run in parallel for almost 20 years. The Berkeley-based Apollo team and the Sanger-based Artemis team have in some cases produced clear alternative paradigms for viewing and annotating genome data but a more predominant theme has been convergence in purpose and approach. A particular strength of the Apollo system is its performance, scalability, and interoperability. We will build upon Apollo infrastructure to include components that have been essential to Artemis users and have been frequently requested by the Apollo community. These will include developing "snap-to-grid" functionality that auto-aligns exons to reading frames during interactive editing; support for small-scale users to load draft annotated genomes from a file, make changes and store them in the same file (a highly used feature of Artemis); and parallel viewing of the same sequence at two zoom levels. The Artemis Comparison Tool is built upon Artemis software and enable comparative genomics data and synteny to be explored in the context of genome annotation. We will include ACT-influenced views into the new Apollo. Moreover, adaptors will be created that allow Apollo to present genome annotation and comparative views directly from Ensembl databases and APIs. This will enable multiple users to remotely perform fast synteny-guided annotation of multiple genomes, in a way that was only previously possible for small genomes using local edited flat-files.

The new Apollo will replace the existing Artemis and Apollo projects and lead to collaborative development and long term sustainability. This tool will support scalable short-term annotation projects as well as long-term curation, enabling non-experts to annotate and curate across the full range of sequenced genomes.

The primary beneficiaries of this work will be genomic scientists in academic and industrial research and in education. In a research context, the tool will be used by professional annotators ("biocurators") during genome projects, to edit automated annotation of gene models, and to update and improve those annotations based on new evidence. Due to the increasing number of species that require curatorial attention, it is vitally important that expertise is shared as broadly as possible; combining the two major annotation tools into a single new generation tool will allow convergence in the way genomes are annotated and curated, helping to solidify and establish best practices for professional biocuration. The software will also encourage participation in genome annotation by researchers who are interested in a particular species (and may be domain experts in that species) but are not professional biocurators; for example, members of the research communities that work with that species and so are downstream users of the gene models being produced. Because the tool is based on a popular browser with a well-established "look and feel", most users should find creating or editing annotation intuitive and satisfying.

The current Artemis and Apollo tools are used extensively for teaching purposes, as well as research. Several projects in the US have incorporated Apollo into undergraduate teaching and Artemis has been an integral part of bioinformatics training workshops for several thousand junior researchers around the world. Artemis has also been used in an engagement project involving more than 70 UK schools. For many students at all levels, experiencing genome annotation first hand is eye opening way to understand common concepts in genomics, genetics and molecular biology. In the proposed work a new generation annotation tool will be produced, merging existing annotation paradigms. This will enable a greater convergence in teaching approaches - it will no longer be necessary to train two independent communities. This will simplify the field from a student perspective and bring two communities of genome scientists together.