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Data Mining Techniques for the Life Sciences pp 211–223Cite as

Systematic Exploration of an Efficient Amino Acid Substitution Matrix: MIQS

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1415))

Abstract

Amino acid sequence comparisons to find similarities between proteins are fundamental sequence information analyses for inferring protein structure and function. In this study, we improve amino acid substitution matrices to identify distantly related proteins. We systematically sampled and benchmarked substitution matrices generated from the principal component analysis (PCA) subspace based on a set of typical existing matrices. Based on the benchmark results, we identified a region of highly sensitive matrices in the PCA subspace using kernel density estimation (KDE). Using the PCA subspace, we were able to deduce a novel sensitive matrix, called MIQS, which shows better detection performance for detecting distantly related proteins than those of existing matrices. This approach to derive an efficient amino acid substitution matrix might influence many fields of protein sequence analysis. MIQS is available at http://csas.cbrc.jp/Ssearch/.

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Abbreviations

AUC :

Area under the ROC curve

BLOSUM :

Block substitution matrix

KDE :

Kernel density estimation

MIQS :

Matrix to improve quality in similarity search

PCA :

Principal component analysis

ROC :

Receiver operating characteristic

VTML :

Variable time maximum likelihood

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Acknowledgments

This work was partially supported by Platform Project for Supporting in Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, and Structural Life Science) from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) and Japan Agency for Medical Research and Development (AMED). We thank Drs. Somlata Gupta, Kumiko Nakada-Tsukui, and Tomoyoshi Nozaki of NIID for discussions related to IMD/I-BAR domains in E. histolytica. We thank Toshiyuki Oda for conducting the HHblits search.

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Authors and Affiliations

  1. Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-Ku, Tokyo, 135-0064, Japan

    Kentaro Tomii & Kazunori Yamada

  2. Graduate School of Information Sciences, Tohoku University, 6-3-9 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan

    Kazunori Yamada

Authors
  1. Kentaro Tomii
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  2. Kazunori Yamada
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Corresponding author

Correspondence to Kentaro Tomii .

Editor information

Editors and Affiliations

  1. Max F. Perutz Laboratories GmbH, Universität Wien, Wien, Austria

    Oliviero Carugo

  2. Technology and Research (A*STAR), Agency for Science, Singapore, Singapore

    Frank Eisenhaber

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Tomii, K., Yamada, K. (2016). Systematic Exploration of an Efficient Amino Acid Substitution Matrix: MIQS. In: Carugo, O., Eisenhaber, F. (eds) Data Mining Techniques for the Life Sciences. Methods in Molecular Biology, vol 1415. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3572-7_11

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  • DOI: https://doi.org/10.1007/978-1-4939-3572-7_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3570-3

  • Online ISBN: 978-1-4939-3572-7

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