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Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew.
Yu Fan1, Dandan Yu2, Yong-Gang Yao3
11] 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.
Scientific Reports
|November 22, 2014
Summary
The Tree shrew Database (TreeshrewDB) offers an accessible, annotated genome for Tupaia belangeri, a primate model organism. This resource aids biomedical research by integrating gene data, expression patterns, and analysis tools.
Area of Science:
- Genomics
- Bioinformatics
- Comparative Genomics
Background:
- The tree shrew (Tupaia belangeri) is evolutionarily close to primates, making it a valuable model organism for biomedical research.
- The availability of a high-quality Chinese tree shrew genome has increased interest in its use as an experimental model.
- Efficient access to comprehensive genomic data is crucial for advancing tree shrew-based research.
Purpose of the Study:
- To create a user-friendly, web-based platform for accessing and analyzing the tree shrew genome.
- To integrate updated gene sets, functional annotations, and mRNA expression data.
- To provide integrated bioinformatics tools for gene sequence analysis and evolutionary studies.
Main Methods:
- Development of the Tree shrew Database (TreeshrewDB) as a web platform.
- Integration of existing tree shrew genome data, including an updated gene set.
- Incorporation of functional annotation, mRNA expression patterns, and bioinformatics tools (Blast, Muscle, GBrowse, GeneWise, codeml).
- Development of a pipeline for positive selection analysis.
Main Results:
- TreeshrewDB provides a centralized and accessible resource for tree shrew genomic information.
- The platform integrates diverse datasets, including gene annotations and expression profiles.
- Includes integrated tools for sequence analysis and evolutionary studies, such as positive selection analysis.
Conclusions:
- TreeshrewDB offers a valuable, user-friendly resource for the scientific community studying the tree shrew model organism.
- The database facilitates research in various biological fields by simplifying access to genomic data and analysis tools.
- This resource is expected to significantly advance biomedical research utilizing the tree shrew.
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