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Efficient algorithms for identifying orthologous simple sequence repeats of disease genes

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Abstract

Dynamic mutations of simple sequence repeats (SSRs) have been demonstrated to affect normal gene function and cause different genetic disorders. Several conserved and even partial functional SSR patterns are discovered in inherited orthologous disease genes. To explore a wide range of SSRs in genetic diseases, a comprehensive system focusing on identifying orthologous SSRs of disease genes through a comparative genomics mechanism is constructed and accomplished by adopting online Mendelian inheritance in man (OMIM) and NCBI HomoloGene databases as the fundamental resources of human genetic diseases and homologous gene information. In addition, an efficient and effective algorithm for searching SSR patterns is also developed for providing annotated SSR information among various model species. By integrating these data resources and mining technologies, biologists and doctors can systematically retrieve novel and important conserved SSR information among orthologous disease genes. The proposed system, Orthologous SSR for Disease Genes (OSDG), is the first comprehensive framework for identifying orthologous SSRs as potential causative factors of genetic disorders and is freely available at http://osdg.cs.ntou.edu.tw/.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan

    Chienming Chen, Chihchia Chen, Tsanhuang Shih & Tunwen Pai

  2. Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan

    Chinhua Hu & Wenshyong Tzou

Authors
  1. Chienming Chen
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  2. Chihchia Chen
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  3. Tsanhuang Shih
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  4. Tunwen Pai
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  5. Chinhua Hu
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  6. Wenshyong Tzou
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Corresponding author

Correspondence to Tunwen Pai.

Additional information

This research is supported by the Center for Marine Bioenvironment and Biotechnology (CMBB) in National Taiwan Ocean University, Keelung, Taiwan, and the National Science Council in Taiwan (NSC97-2627-B-019-003).

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Chen, C., Chen, C., Shih, T. et al. Efficient algorithms for identifying orthologous simple sequence repeats of disease genes. J Syst Sci Complex 23, 906–916 (2010). https://doi.org/10.1007/s11424-010-0203-2

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  • DOI: https://doi.org/10.1007/s11424-010-0203-2

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