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

Publication Type:Journal Article
Year of Publication:2018
Authors:A. Rozanski, Brandl, H., Moon, H. K., Grohme, M. A., Henry, I., Rink, J. C., Martin-Duran, J. M., Hüttner, K., Bartscherer, K.
Journal:Nucleic Acids Researchnar
Pagination:D812 - D820
Date Published:2018
ISBN Number:0305-1048

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 ( 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.

Short Title:Nucleic Acids Research
Sun, 2019-03-31 17:07 -- Eduard
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith