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AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes

Current 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 gen...

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Autores principales: Triant, Deborah A., Walsh, Amy T., Hartley, Gabrielle A., Petry, Bruna, Stegemiller, Morgan R., Nelson, Benjamin M., McKendrick, Makenna M., Fuller, Emily P., Cockett, Noelle E., Koltes, James E., McKay, Stephanie D., Green, Jonathan A., Murdoch, Brenda M., Hagen, Darren E., Elsik, Christine G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10382368/
https://www.ncbi.nlm.nih.gov/pubmed/37460664
http://dx.doi.org/10.1007/s00335-023-10008-1
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author Triant, Deborah A.
Walsh, Amy T.
Hartley, Gabrielle A.
Petry, Bruna
Stegemiller, Morgan R.
Nelson, Benjamin M.
McKendrick, Makenna M.
Fuller, Emily P.
Cockett, Noelle E.
Koltes, James E.
McKay, Stephanie D.
Green, Jonathan A.
Murdoch, Brenda M.
Hagen, Darren E.
Elsik, Christine G.
author_facet Triant, Deborah A.
Walsh, Amy T.
Hartley, Gabrielle A.
Petry, Bruna
Stegemiller, Morgan R.
Nelson, Benjamin M.
McKendrick, Makenna M.
Fuller, Emily P.
Cockett, Noelle E.
Koltes, James E.
McKay, Stephanie D.
Green, Jonathan A.
Murdoch, Brenda M.
Hagen, Darren E.
Elsik, Christine G.
author_sort Triant, Deborah A.
collection PubMed
description Current 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00335-023-10008-1.
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spelling pubmed-103823682023-07-30 AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes Triant, Deborah A. Walsh, Amy T. Hartley, Gabrielle A. Petry, Bruna Stegemiller, Morgan R. Nelson, Benjamin M. McKendrick, Makenna M. Fuller, Emily P. Cockett, Noelle E. Koltes, James E. McKay, Stephanie D. Green, Jonathan A. Murdoch, Brenda M. Hagen, Darren E. Elsik, Christine G. Mamm Genome Article Current 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00335-023-10008-1. Springer US 2023-07-17 2023 /pmc/articles/PMC10382368/ /pubmed/37460664 http://dx.doi.org/10.1007/s00335-023-10008-1 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Triant, Deborah A.
Walsh, Amy T.
Hartley, Gabrielle A.
Petry, Bruna
Stegemiller, Morgan R.
Nelson, Benjamin M.
McKendrick, Makenna M.
Fuller, Emily P.
Cockett, Noelle E.
Koltes, James E.
McKay, Stephanie D.
Green, Jonathan A.
Murdoch, Brenda M.
Hagen, Darren E.
Elsik, Christine G.
AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes
title AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes
title_full AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes
title_fullStr AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes
title_full_unstemmed AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes
title_short AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes
title_sort aganimalgenomes: browsers for viewing and manually annotating farm animal genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10382368/
https://www.ncbi.nlm.nih.gov/pubmed/37460664
http://dx.doi.org/10.1007/s00335-023-10008-1
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