title: Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew.
abstract: The tree shrew (Tupaia belangeri) is a small mammal with a close relationship to primates and it has been proposed as an alternative experimental animal to primates in biomedical research. The recent release of a high-quality Chinese tree shrew genome enables more researchers to use this species as the model animal in their studies. With the aim to making the access to an extensively annotated genome database straightforward and easy, we have created the Tree shrew Database (TreeshrewDB). This is a web-based platform that integrates the currently available data from the tree shrew genome, including an updated gene set, with a systematic functional annotation and a mRNA expression pattern. In addition, to assist with automatic gene sequence analysis, we have integrated the common programs Blast, Muscle, GBrowse, GeneWise and codeml, into TreeshrewDB. We have also developed a pipeline for the analysis of positive selection. The user-friendly interface of TreeshrewDB, which is available at http://www.treeshrewdb.org, will undoubtedly help in many areas of biological research into the tree shrew.
authors.affiliation: 1] Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Fan
authors.affiliation: Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China.
authors.forename: Dandan
authors.initials: D
authors.lastname: Yu
authors.affiliation: 1] Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China [3] Kunming Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
authors.forename: Yong-Gang
authors.initials: YG
authors.lastname: Yao
mesh_terms: D000818:Animals; D002681:China; D030541:Databases, Genetic; D016678:Genome; D025341:Principal Component Analysis; D012313:RNA / Q000378:metabolism; D059467:Transcriptome; D014417:Tupaia / Q000235:genetics*
chemical_list: D012313:RNA