ANISEED 2015: a digital framework for the comparative developmental biology of ascidians - PubMed (original) (raw)
. 2016 Jan 4;44(D1):D808-18.
doi: 10.1093/nar/gkv966. Epub 2015 Sep 29.
Cyril Martin 1, Christelle Dantec 1, Delphine Dauga 2, Mickaël Mendez 1, Paul Simion 3, Madeline Percher 1, Baptiste Laporte 4, Céline Scornavacca 3, Anna Di Gregorio 5, Shigeki Fujiwara 6, Mathieu Gineste 1, Elijah K Lowe 7, Jacques Piette 1, Claudia Racioppi 8, Filomena Ristoratore 9, Yasunori Sasakura 10, Naohito Takatori 11, Titus C Brown 12, Frédéric Delsuc 3, Emmanuel Douzery 3, Carmela Gissi 13, Alex McDougall 14, Hiroki Nishida 15, Hitoshi Sawada 16, Billie J Swalla 17, Hitoyoshi Yasuo 14, Patrick Lemaire 18
Affiliations
- PMID: 26420834
- PMCID: PMC4702943
- DOI: 10.1093/nar/gkv966
ANISEED 2015: a digital framework for the comparative developmental biology of ascidians
Matija Brozovic et al. Nucleic Acids Res. 2016.
Abstract
Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.
© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Figures
Figure 1.
Overview of the two main structuring parts in the experiment module.
Figure 2.
The search interface for expression patterns. Note the Anisearch field at the top of the screen, which searches the whole database for keywords, genes, anatomical entities, etc. The expression search interface permits to look for genes expressed in a set of terriories, but whose expression is excluded from another set. Searches can be restricted to a gene, or an article. Gene expression patterns in manipulated embryos can be excluded from the results.
Figure 3.
Screenshot from the ANISEED Ciona intestinalis type A Genome Browser.
Figure 4.
Cladogramme of the species supported with external species used for functional gene annotation purposes. The names of fully supported species with Developmental and Genome browsers are underlined.
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