Refinement of Amino Acid Substitution Matrix for Detecting Distant Relationships of Proteins

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  • YAMADA Kazunori
    Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
  • TOMII Kentaro
    Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)

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Other Title
  • 遠縁タンパク質検索に適した新規アミノ酸置換行列
  • トオエン タンパクシツ ケンサク ニ テキシタ シンキ アミノサン チカン ギョウレツ

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Abstract

Amino acid similarity search methods are fundamental tools for inferring protein structure and function. Optimization of amino acid substitution matrices is indispensable to improve search performance. We explored matrices that are ideal for detecting distantly related proteins in the PCA subspace that represents a set of typical existing matrices, and derived a novel sensitive matrix: MIQS. Test results show that the MIQS detection performance is superior to those of existing matrices and other sequence comparison methods. This refinement of the amino acid substitution matrix might influence many fields of sequence analysis. MIQS is available at http://csas.cbrc.jp/Ssearch/.

Journal

  • Seibutsu Butsuri

    Seibutsu Butsuri 55 (3), 133-136, 2015

    The Biophysical Society of Japan General Incorporated Association

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