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    National Tsing Hua University Institutional Repository > 電機資訊學院 > 資訊工程學系 > 期刊論文 >  RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints


    Please use this identifier to cite or link to this item: http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/66331


    Title: RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
    Authors: Chung, Yun-Sheng;Lee, Wei-Hsun;Tang, Chuan Yi;Lu, Chin Lung
    教師: 唐傳義
    Date: 2007
    Publisher: Oxford University Press
    Relation: Nucleic Acids Research,2007,Vol. 35,No. suppl_2,p W639-W644
    Keywords: PROTEIN SEQUENCES
    DIALIGN
    ALGORITHM
    DNA
    Abstract: RE-MuSiC is a web-based multiple sequence alignment tool that can incorporate biological knowledge about structure, function, or conserved patterns regarding the sequences of interest. It accepts amino acid or nucleic acid sequences and a set of constraints as inputs. The constraints are pattern descriptions, instead of exact positions of fragments to be aligned together. The output is an alignment where for each pattern (constraint), an occurrence on each sequence can be found aligned together with those on the other sequences, in a manner that the overall alignment is optimized. Its predecessor, MuSiC, has been found useful by researchers since its release in 2004. However, it is noticed in applications that the pattern formulation adopted in MuSiC, namely, plain strings allowing mismatches, is not expressive and flexible enough. The constraint formulation adopted in RE-MuSiC is therefore enhanced to be regular expressions, which is convenient in expressing many biologically significant patterns like those collected in the PROSITE database, or structural consensuses that often involve variable ranges between conserved parts. Experiments demonstrate that RE-MuSiC can be used to help predict important residues and locate phylogenetically conserved structural elements. RE-MuSiC is available on-line at http://140.113.239.131/RE-MUSIC.
    URI: http://www.oxfordjournals.org/
    http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/66331
    Appears in Collections:[資訊工程學系] 期刊論文

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