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    National Tsing Hua University Institutional Repository > 電機資訊學院 > 資訊工程學系 > 會議論文  >  An IDC-based algorithm for efficient homology filtration with guaranteed seriate coverage


    Please use this identifier to cite or link to this item: http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/13916


    Title: An IDC-based algorithm for efficient homology filtration with guaranteed seriate coverage
    Authors: Lee,Hsiao Ping
    Shih,Ching Hua
    Tsai,Yin Te
    Sheu,Tzu Fang
    Tang,Chuan Yi
    Date: 2004
    Publisher: Institute of Electrical and Electronics Engineers Computer Society
    Keywords: Genetic engineering
    Algorithms
    Error analysis
    DNA
    RNA
    Database systems
    Proteins
    Diseases
    Abstract: The homology search within genomic databases is a fundamental and crucial work for biological knowledge discovery. With exponentially increasing sizes and accesses of databases, the filtration approach, which filters impossible homology candidates to reduce the time for homology verification, becomes more important in bioinformatics. Most of known gram-based filtration approaches, like QUASAR, in the literature have limited error tolerance and would conduct potentially higher false-positives. In this paper, we present an IDC-based lossless filtration algorithm with guaranteed seriate coverage and error tolerance for efficient homology discovery. In our method, the original work of homology extraction with requested seriate coverage and error levels is transformed to a longest increasing subsequence problem with range constraints, and an efficient algorithm is proposed for the problem in this paper. The experimental results show that the method significantly outperforms QUASAR. On some comparable sensitivity levels, our homology filter would make the discovery more than three orders of magnitude faster than that QUASAR does, and more than four orders faster than the exhaustive search.
    Relation Link: Bioinformatics and Bioengineering, 2004. BIBE 2004. Proceedings. Fourth IEEE Symposium on 19-21 May 2004 Page(s):395 - 402
    http://webservices.ieee.org/pindex_basic.html
    URI: http://nthur.lib.nthu.edu.tw/handle/987654321/13916
    Appears in Collections:[資訊工程學系] 會議論文
    [資訊系統與應用研究所] 會議論文
    [電腦與通訊科技研發中心] 會議論文
    [腦科學研究中心] 會議論文

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