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Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome
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| Zeitschriftentitel: | Animal Genetics |
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| Personen und Körperschaften: | , , , , , , , , , , , , , , , , , , , , |
| In: | Animal Genetics, 51, 2020, 5, S. 675-682 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Wiley
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| Schlagwörter: |
| author_facet |
Triant, D. A. Le Tourneau, J. J. Diesh, C. M. Unni, D. R. Shamimuzzaman, M. Walsh, A. T. Gardiner, J. Goldkamp, A. K. Li, Y. Nguyen, H. N. Roberts, C. Zhao, Z. Alexander, L. J. Decker, J. E. Schnabel, R. D. Schroeder, S. G. Sonstegard, T. S. Taylor, J. F. Rivera, R. M. Hagen, D. E. Elsik, C. G. Triant, D. A. Le Tourneau, J. J. Diesh, C. M. Unni, D. R. Shamimuzzaman, M. Walsh, A. T. Gardiner, J. Goldkamp, A. K. Li, Y. Nguyen, H. N. Roberts, C. Zhao, Z. Alexander, L. J. Decker, J. E. Schnabel, R. D. Schroeder, S. G. Sonstegard, T. S. Taylor, J. F. Rivera, R. M. Hagen, D. E. Elsik, C. G. |
|---|---|
| author |
Triant, D. A. Le Tourneau, J. J. Diesh, C. M. Unni, D. R. Shamimuzzaman, M. Walsh, A. T. Gardiner, J. Goldkamp, A. K. Li, Y. Nguyen, H. N. Roberts, C. Zhao, Z. Alexander, L. J. Decker, J. E. Schnabel, R. D. Schroeder, S. G. Sonstegard, T. S. Taylor, J. F. Rivera, R. M. Hagen, D. E. Elsik, C. G. |
| spellingShingle |
Triant, D. A. Le Tourneau, J. J. Diesh, C. M. Unni, D. R. Shamimuzzaman, M. Walsh, A. T. Gardiner, J. Goldkamp, A. K. Li, Y. Nguyen, H. N. Roberts, C. Zhao, Z. Alexander, L. J. Decker, J. E. Schnabel, R. D. Schroeder, S. G. Sonstegard, T. S. Taylor, J. F. Rivera, R. M. Hagen, D. E. Elsik, C. G. Animal Genetics Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome Genetics Animal Science and Zoology General Medicine |
| author_sort |
triant, d. a. |
| spelling |
Triant, D. A. Le Tourneau, J. J. Diesh, C. M. Unni, D. R. Shamimuzzaman, M. Walsh, A. T. Gardiner, J. Goldkamp, A. K. Li, Y. Nguyen, H. N. Roberts, C. Zhao, Z. Alexander, L. J. Decker, J. E. Schnabel, R. D. Schroeder, S. G. Sonstegard, T. S. Taylor, J. F. Rivera, R. M. Hagen, D. E. Elsik, C. G. 0268-9146 1365-2052 Wiley Genetics Animal Science and Zoology General Medicine http://dx.doi.org/10.1111/age.12962 <jats:title>Summary</jats:title><jats:p>With the availability of a new highly contiguous <jats:italic>Bos taurus</jats:italic> reference genome assembly (ARS‐UCD1.2), it is the opportune time to upgrade the bovine gene set by seeking input from researchers. Furthermore, advances in graphical genome annotation tools now make it possible for researchers to leverage sequence data generated with the latest technologies to collaboratively curate genes. For many years the Bovine Genome Database (BGD) has provided tools such as the <jats:sc>Apollo</jats:sc> genome annotation editor to support manual bovine gene curation. The goal of this paper is to explain the reasoning behind the decisions made in the manual gene curation process while providing examples using the existing BGD tools. We will describe the sources of gene annotation evidence provided at the BGD, including RNA‐seq and Iso‐Seq data. We will also explain how to interpret various data visualizations when curating gene models, and will demonstrate the value of manual gene annotation. The process described here can be applied to manual gene curation for other species with similar tools. With a better understanding of manual gene annotation, researchers will be encouraged to edit gene models and contribute to the enhancement of livestock gene sets.</jats:p> Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome Animal Genetics |
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| title |
Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| title_unstemmed |
Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| title_full |
Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| title_fullStr |
Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| title_full_unstemmed |
Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| title_short |
Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| title_sort |
using online tools at the bovine genome database to manually annotate genes in the new reference genome |
| topic |
Genetics Animal Science and Zoology General Medicine |
| url |
http://dx.doi.org/10.1111/age.12962 |
| publishDate |
2020 |
| physical |
675-682 |
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<jats:title>Summary</jats:title><jats:p>With the availability of a new highly contiguous <jats:italic>Bos taurus</jats:italic> reference genome assembly (ARS‐UCD1.2), it is the opportune time to upgrade the bovine gene set by seeking input from researchers. Furthermore, advances in graphical genome annotation tools now make it possible for researchers to leverage sequence data generated with the latest technologies to collaboratively curate genes. For many years the Bovine Genome Database (BGD) has provided tools such as the <jats:sc>Apollo</jats:sc> genome annotation editor to support manual bovine gene curation. The goal of this paper is to explain the reasoning behind the decisions made in the manual gene curation process while providing examples using the existing BGD tools. We will describe the sources of gene annotation evidence provided at the BGD, including RNA‐seq and Iso‐Seq data. We will also explain how to interpret various data visualizations when curating gene models, and will demonstrate the value of manual gene annotation. The process described here can be applied to manual gene curation for other species with similar tools. With a better understanding of manual gene annotation, researchers will be encouraged to edit gene models and contribute to the enhancement of livestock gene sets.</jats:p> |
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| author | Triant, D. A., Le Tourneau, J. J., Diesh, C. M., Unni, D. R., Shamimuzzaman, M., Walsh, A. T., Gardiner, J., Goldkamp, A. K., Li, Y., Nguyen, H. N., Roberts, C., Zhao, Z., Alexander, L. J., Decker, J. E., Schnabel, R. D., Schroeder, S. G., Sonstegard, T. S., Taylor, J. F., Rivera, R. M., Hagen, D. E., Elsik, C. G. |
| author_facet | Triant, D. A., Le Tourneau, J. J., Diesh, C. M., Unni, D. R., Shamimuzzaman, M., Walsh, A. T., Gardiner, J., Goldkamp, A. K., Li, Y., Nguyen, H. N., Roberts, C., Zhao, Z., Alexander, L. J., Decker, J. E., Schnabel, R. D., Schroeder, S. G., Sonstegard, T. S., Taylor, J. F., Rivera, R. M., Hagen, D. E., Elsik, C. G., Triant, D. A., Le Tourneau, J. J., Diesh, C. M., Unni, D. R., Shamimuzzaman, M., Walsh, A. T., Gardiner, J., Goldkamp, A. K., Li, Y., Nguyen, H. N., Roberts, C., Zhao, Z., Alexander, L. J., Decker, J. E., Schnabel, R. D., Schroeder, S. G., Sonstegard, T. S., Taylor, J. F., Rivera, R. M., Hagen, D. E., Elsik, C. G. |
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| description | <jats:title>Summary</jats:title><jats:p>With the availability of a new highly contiguous <jats:italic>Bos taurus</jats:italic> reference genome assembly (ARS‐UCD1.2), it is the opportune time to upgrade the bovine gene set by seeking input from researchers. Furthermore, advances in graphical genome annotation tools now make it possible for researchers to leverage sequence data generated with the latest technologies to collaboratively curate genes. For many years the Bovine Genome Database (BGD) has provided tools such as the <jats:sc>Apollo</jats:sc> genome annotation editor to support manual bovine gene curation. The goal of this paper is to explain the reasoning behind the decisions made in the manual gene curation process while providing examples using the existing BGD tools. We will describe the sources of gene annotation evidence provided at the BGD, including RNA‐seq and Iso‐Seq data. We will also explain how to interpret various data visualizations when curating gene models, and will demonstrate the value of manual gene annotation. The process described here can be applied to manual gene curation for other species with similar tools. With a better understanding of manual gene annotation, researchers will be encouraged to edit gene models and contribute to the enhancement of livestock gene sets.</jats:p> |
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| spelling | Triant, D. A. Le Tourneau, J. J. Diesh, C. M. Unni, D. R. Shamimuzzaman, M. Walsh, A. T. Gardiner, J. Goldkamp, A. K. Li, Y. Nguyen, H. N. Roberts, C. Zhao, Z. Alexander, L. J. Decker, J. E. Schnabel, R. D. Schroeder, S. G. Sonstegard, T. S. Taylor, J. F. Rivera, R. M. Hagen, D. E. Elsik, C. G. 0268-9146 1365-2052 Wiley Genetics Animal Science and Zoology General Medicine http://dx.doi.org/10.1111/age.12962 <jats:title>Summary</jats:title><jats:p>With the availability of a new highly contiguous <jats:italic>Bos taurus</jats:italic> reference genome assembly (ARS‐UCD1.2), it is the opportune time to upgrade the bovine gene set by seeking input from researchers. Furthermore, advances in graphical genome annotation tools now make it possible for researchers to leverage sequence data generated with the latest technologies to collaboratively curate genes. For many years the Bovine Genome Database (BGD) has provided tools such as the <jats:sc>Apollo</jats:sc> genome annotation editor to support manual bovine gene curation. The goal of this paper is to explain the reasoning behind the decisions made in the manual gene curation process while providing examples using the existing BGD tools. We will describe the sources of gene annotation evidence provided at the BGD, including RNA‐seq and Iso‐Seq data. We will also explain how to interpret various data visualizations when curating gene models, and will demonstrate the value of manual gene annotation. The process described here can be applied to manual gene curation for other species with similar tools. With a better understanding of manual gene annotation, researchers will be encouraged to edit gene models and contribute to the enhancement of livestock gene sets.</jats:p> Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome Animal Genetics |
| spellingShingle | Triant, D. A., Le Tourneau, J. J., Diesh, C. M., Unni, D. R., Shamimuzzaman, M., Walsh, A. T., Gardiner, J., Goldkamp, A. K., Li, Y., Nguyen, H. N., Roberts, C., Zhao, Z., Alexander, L. J., Decker, J. E., Schnabel, R. D., Schroeder, S. G., Sonstegard, T. S., Taylor, J. F., Rivera, R. M., Hagen, D. E., Elsik, C. G., Animal Genetics, Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome, Genetics, Animal Science and Zoology, General Medicine |
| title | Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| title_full | Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| title_fullStr | Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| title_full_unstemmed | Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| title_short | Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| title_sort | using online tools at the bovine genome database to manually annotate genes in the new reference genome |
| title_unstemmed | Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome |
| topic | Genetics, Animal Science and Zoology, General Medicine |
| url | http://dx.doi.org/10.1111/age.12962 |