A treatable interface for MTRAP sequence alignment method
Article No.: 102, Pages 1 - 2
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
[1]
G. Blackshields, I. Wallace, M. Larkin, and D. Higgins. Analysis and comparison of benchmarks for multiple sequence alignment. In Silico Biology, 6(4):321--339, 2006.
[2]
R. C. Edgar. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32:1792--1797, 2004.
[3]
D. Feng and R. Doolittle. Progressive sequence alignment as a prerequisitetto correct phylogenetic trees. J. Mol. Evo., 25(4):351--360, 1987.
[4]
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.
[5]
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.
[6]
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.
[7]
K. Katoh, K. Misawa, K. Kuma, and T. Miyata. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30:3059--3066, Jul 2002.
[8]
K. Mizuguchi, C. M. Deane, T. L. Blundell, and J. P. Overington. HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci., 7:2469--2471, Nov 1998.
[9]
C. Notredame, D. G. Higgins, and J. Heringa. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302:205--217, Sep 2000.
[10]
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.
Index Terms
- A treatable interface for MTRAP sequence alignment method
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Published In
October 2011
949 pages
ISBN:9781450309134
DOI:10.1145/2093698
- Conference Chair:
- Simone Frattasi,
- Program Chair:
- Nicola Marchetti
Copyright © 2011 ACM.
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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
Publisher
Association for Computing Machinery
New York, NY, United States
Publication History
Published: 26 October 2011
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- Research-article
Conference
ISABEL '11
Sponsor:
- Technical University of Catalonia Spain
- River Publishers
- CTTC
- CTIF
ISABEL '11: International Symposium on Applied Sciences in Biomedical and Communication Technologies
October 26 - 29, 2011
Barcelona, Spain
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