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  PlanMine 3.0improvements to a mineable resource of flatworm biology and biodiversity.

Rozanski, A., Moon, H., Brandl, H., Martin-Duran, J. M., Grohme, M. A., Hüttner, K., et al. (2019). PlanMine 3.0improvements to a mineable resource of flatworm biology and biodiversity. Nucleic Acids Research, 47(D1), D812-D820. doi:10.1093/nar/gky1070.

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 Creators:
Rozanski, A., Author
Moon, H., Author
Brandl, H., Author
Martin-Duran, J. M., Author
Grohme, M. A., Author
Hüttner, K., Author
Bartscherer, K., Author
Henry, I., Author
Rink, J. C.1, Author              
Affiliations:
1Department of Tissue Dynamics and Regeneration, MPI for Biophysical Chemistry, Max Planck Society, ou_3181978              

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 Abstract: Flatworms (Platyhelminthes) are a basally branching phylum that harbours a wealth of fascinating biology, including planarians with their astonishing regenerative abilities and the parasitic tape worms and blood flukes that exert a massive impact on human health. PlanMine (http://planmine.mpi-cbg.de/) has the mission objective of providing both a mineable sequence repository for planarians and also a resource for the comparative analysis of flatworm biology. While the original PlanMine release was entirely based on transcriptomes, the current release transitions to a more genomic perspective. Building on the recent availability of a high quality genome assembly of the planarian model species Schmidtea mediterranea, we provide a gene prediction set that now assign existing transcripts to defined genomic coordinates. The addition of recent single cell and bulk RNA-seq datasets greatly expands the available gene expression information. Further, we add transcriptomes from a broad range of other flatworms and provide a phylogeny-aware interface that makes evolutionary species comparisons accessible to non-experts. At its core, PlanMine continues to utilize the powerful InterMine framework and consistent data annotations to enable meaningful inter-species comparisons. Overall, PlanMine 3.0 thus provides a host of new features that makes the fascinating biology of flatworms accessible to the wider research community.

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Language(s): eng - English
 Dates: 2018-11-282019-01-08
 Publication Status: Published in print
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 Rev. Type: Peer
 Identifiers: DOI: 10.1093/nar/gky1070
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Title: Nucleic Acids Research
Source Genre: Journal
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Pages: - Volume / Issue: 47 (D1) Sequence Number: - Start / End Page: D812 - D820 Identifier: -