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A treatable interface for MTRAP sequence alignment method

Published: 26 October 2011 Publication History

Abstract

In the last ISABEL, we showed a high quality sequence alignment method called MTRAP. Although there exists a need for high quality alignment, a treatable alignment software, as typified by ClustalW, is also essential for the analysis estimating the function of gene or to seek mechanism of molecular interactions. In this paper, we develop a new treatable interface software for the MTRAP alignment. Moreover, we show that the alignment accuracy could be improved by our approach not only for pairwise sequences but also multiple sequences.

References

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R. C. Edgar. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32:1792--1797, 2004.
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G. Gonnet, M. Cohen, and S. Benner. Analysis of amino acid substitution during divergent evolution: the 400 by 400 dipeptide substitution matrix. BBRC, 199:489--489, 1994.
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T. Hara, K. Sato, and M. Ohya. Mtrap: pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues. BMC Bioinformatics, 11:235, 2010.
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T. Hara, K. Sato, and M. Ohya. New sequence alignment by a measure due to entangled correlation in two consecutive residues. In 3rd ISABEL Proc., Center for Ecclesiastical Services, Rome, Italy, November 2010. ISABEL 2010.
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J. D. Thompson, D. G. Higgins, and T. J. Gibson. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22:4673--4680, Nov 1994.

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  1. A treatable interface for MTRAP sequence alignment method

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        cover image ACM Other conferences
        ISABEL '11: Proceedings of the 4th International Symposium on Applied Sciences in Biomedical and Communication Technologies
        October 2011
        949 pages
        ISBN:9781450309134
        DOI:10.1145/2093698
        Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

        Sponsors

        • Universitat Pompeu Fabra
        • IEEE
        • Technical University of Catalonia Spain: Technical University of Catalonia (UPC), Spain
        • River Publishers: River Publishers
        • CTTC: Technological Center for Telecommunications of Catalonia
        • CTIF: Kyranova Ltd, Center for TeleInFrastruktur

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        Association for Computing Machinery

        New York, NY, United States

        Publication History

        Published: 26 October 2011

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