AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes
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Published:2023-07-17
Issue:3
Volume:34
Page:418-436
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ISSN:0938-8990
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Container-title:Mammalian Genome
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language:en
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Short-container-title:Mamm Genome
Author:
Triant Deborah A., Walsh Amy T.ORCID, Hartley Gabrielle A.ORCID, Petry BrunaORCID, Stegemiller Morgan R.ORCID, Nelson Benjamin M.ORCID, McKendrick Makenna M.ORCID, Fuller Emily P.ORCID, Cockett Noelle E., Koltes James E.ORCID, McKay Stephanie D.ORCID, Green Jonathan A.ORCID, Murdoch Brenda M.ORCID, Hagen Darren E.ORCID, Elsik Christine G.ORCID
Abstract
AbstractCurrent genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific gene features in the genomes. Here we present genome visualization and annotation tools to support seven livestock species (bovine, chicken, goat, horse, pig, sheep, and water buffalo), available in a new resource called AgAnimalGenomes. In addition to supporting the manual refinement of gene models, these browsers provide visualization tracks for hundreds of RNAseq experiments, as well as data generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. For species with predicted gene sets from both Ensembl and RefSeq, the browsers provide special tracks showing the thousands of protein-coding genes that disagree across the two gene sources, serving as a valuable resource to alert researchers to gene model issues that may affect data interpretation. We describe the data and search methods available in the new genome browsers and how to use the provided tools to edit and create new gene models.
Funder
National Institute of Food and Agriculture National Science Foundation
Publisher
Springer Science and Business Media LLC
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