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MnTEdb, a collective resource for mulberry transposable elements
Mulberry has been used as an economically important food crop for the domesticated silkworm for thousands of years, resulting in one of the oldest and well-known plant-herbivore interactions. The genome of Morus notabilis has now been sequenced and there is an opportunity to mine the transposable el...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343074/ https://www.ncbi.nlm.nih.gov/pubmed/25725060 http://dx.doi.org/10.1093/database/bav004 |
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author | Ma, Bi Li, Tian Xiang, Zhonghuai He, Ningjia |
author_facet | Ma, Bi Li, Tian Xiang, Zhonghuai He, Ningjia |
author_sort | Ma, Bi |
collection | PubMed |
description | Mulberry has been used as an economically important food crop for the domesticated silkworm for thousands of years, resulting in one of the oldest and well-known plant-herbivore interactions. The genome of Morus notabilis has now been sequenced and there is an opportunity to mine the transposable element (TE) data. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the mulberry genome, a specific, comprehensive and user-friendly web-based database, MnTEdb, was constructed. It was built based on a detailed and accurate identification of all TEs in mulberry. A total of 5925 TEs belonging to 13 superfamilies and 1062 families were deposited in this database. MnTEdb enables users to search, browse and download the mulberry TE sequences. Meanwhile, data mining tools, including BLAST, GetORF, HMMER, Sequence Extractor and JBrowse were also integrated into MnTEdb. MnTEdb will assist researchers to efficiently take advantage of our newly annotated TEs, which facilitate their studies in the origin, amplification and evolution of TEs, as well as the comparative analysis among the different species. Database URL: http://morus.swu.edu.cn/mntedb/ |
format | Online Article Text |
id | pubmed-4343074 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-43430742015-03-17 MnTEdb, a collective resource for mulberry transposable elements Ma, Bi Li, Tian Xiang, Zhonghuai He, Ningjia Database (Oxford) Database Tool Mulberry has been used as an economically important food crop for the domesticated silkworm for thousands of years, resulting in one of the oldest and well-known plant-herbivore interactions. The genome of Morus notabilis has now been sequenced and there is an opportunity to mine the transposable element (TE) data. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the mulberry genome, a specific, comprehensive and user-friendly web-based database, MnTEdb, was constructed. It was built based on a detailed and accurate identification of all TEs in mulberry. A total of 5925 TEs belonging to 13 superfamilies and 1062 families were deposited in this database. MnTEdb enables users to search, browse and download the mulberry TE sequences. Meanwhile, data mining tools, including BLAST, GetORF, HMMER, Sequence Extractor and JBrowse were also integrated into MnTEdb. MnTEdb will assist researchers to efficiently take advantage of our newly annotated TEs, which facilitate their studies in the origin, amplification and evolution of TEs, as well as the comparative analysis among the different species. Database URL: http://morus.swu.edu.cn/mntedb/ Oxford University Press 2015-02-27 /pmc/articles/PMC4343074/ /pubmed/25725060 http://dx.doi.org/10.1093/database/bav004 Text en © The Author(s) 2015. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Tool Ma, Bi Li, Tian Xiang, Zhonghuai He, Ningjia MnTEdb, a collective resource for mulberry transposable elements |
title | MnTEdb, a collective resource for mulberry transposable elements |
title_full | MnTEdb, a collective resource for mulberry transposable elements |
title_fullStr | MnTEdb, a collective resource for mulberry transposable elements |
title_full_unstemmed | MnTEdb, a collective resource for mulberry transposable elements |
title_short | MnTEdb, a collective resource for mulberry transposable elements |
title_sort | mntedb, a collective resource for mulberry transposable elements |
topic | Database Tool |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343074/ https://www.ncbi.nlm.nih.gov/pubmed/25725060 http://dx.doi.org/10.1093/database/bav004 |
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