Dataset Persistent ID
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doi:10.15454/INYUVZ |
Publication Date
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2018-10-04 |
Title
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Transposable element annotation of Arabidopsis lyrata subsp. lyrata
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Link to data
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http://urgi.versailles.inra.fr/repetdb/begin.do#search?taxonGroup=81972
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Author
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Quesneville, Hadi (INRA - Institut National de la Recherche Agronomique) - ORCID: https://orcid.org/0000-0003-3001-4908
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Contact
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Use email button above to contact.
Quesneville, Hadi (INRA - Institut National de la Recherche Agronomique)
URGI (INRA - Institut National de la Recherche Agronomique)
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Description
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After running the TEdenovo, we got a filtered library (without the SSR consensus and without the unclassified consensus if they were generated with less than 10 HSPs). We have clustered this library and the cluster number is in the header of each consensus. After a first TEannot on this library, we filtered the consensus having at least one FLC (Full Length Copy). This library is inserted in RepetDB. We have launched a second TEannot on this library, and we have inserted the statistical data of this second annotation. Be careful, this TE library have not been manually curated. It is provided “as is”, i.e. a direct output of the REPET pipeline. Genome annotation files and TE consensus ID mapping between previous and new classification are available for download. (2017-08-25)
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Kind of Data
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Dataset
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Data Origin
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analysis data
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Subject
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Omics; Plant Breeding and Plant Products
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Life cycle step
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Original release
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Keyword
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transposable_element (SO:0000101) (Sequence Ontology) http://www.sequenceontology.org
Molecular Sequence Annotation (MeSH) https://www.ncbi.nlm.nih.gov/mesh
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Topic Classification
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Genomics (MeSH) https://www.ncbi.nlm.nih.gov/mesh
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Language
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English
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Producer
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Research Unit of Genomics Info (INRA - Institut National de la Recherche Agronomique) (URGI) https://urgi.versailles.inra.fr 
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Production Date
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2017-08-25
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Production Place
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Versailles, France
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Depositor
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Amselem, Joelle
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Deposit Date
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2018-09-25
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Software
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REPET TEdenovo0 Version: 2.5
REPET TEannot0 Version: 2.5
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Data Sources
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Arabidopsis lyrata genome assembly v1.0 (GenBank assembly accession: GCA_000004255.1)
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Origin of Sources
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https://www.ncbi.nlm.nih.gov/assembly/?term=GCA_000004255.1
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