GA Generates New Amino Acid Indices through Comparison between Native and Random Sequences

• Item type: Trans(1)
• 公開日: 2000-11-15
• タイトル: GA Generates New Amino Acid Indices through Comparison between Native and Random Sequences
• タイトル / 言語: en
• タイトル: GA Generates New Amino Acid Indices through Comparison between Native and Random Sequences
• 言語: eng
• キーワード / 主題Scheme: Other
• キーワード / 主題: オリジナル論文
• 資源タイプ / 資源タイプ識別子: http://purl.org/coar/resource_type/c_6501
• 資源タイプ: journal article
• 著者所属: Department of Bioinformatics Biomolecular Engineering Research Institute/Presently with PharmaDesign Inc.
• 著者所属: Department of Bioinformatics Biomolecular Engineering Research Institute
• 著者所属(英): en
• 著者所属(英): Department of Bioinformatics, Biomolecular Engineering Research Institute/Presently with PharmaDesign, Inc.
• 著者所属(英): en
• 著者所属(英): Department of Bioinformatics, Biomolecular Engineering Research Institute
• 著者名: Satoru, Kanai; Hiroyuki, Toh
• 著者名(英): Satoru, Kanai; Hiroyuki, Toh
• 論文抄録 / 内容記述タイプ: Other
• 論文抄録 / 内容記述: The amino acid sequence of a protein carries its folding information. If the information is encoded by the arrangement of the amino acid residues along the primary structure the random shuffling of the residues would degrade the information. We developed a new method to compare the native sequence with random sequences generated from the native sequence in order to extract such information. First amino acid indices were randomly generated. That is the initial indices have no significance on the feature of residues. Next using the indices the averaged distance between a native sequence and the random sequences was calculated based on the autoregressive (AR) analysis and the linear predictive coding (LPC) cepstrum analysis. The indices were subjected to the genetic algorithm (GA) using the distance as the fitness so that the distance between the native sequence and the random sequences becomes larger. We found that the indices converged to hydrophobicity indices by the GA operation. The AR analysis with the converged indices revealed that the autocorrelation in the native sequence is related to the secondary structure.
• 論文抄録(英) / 内容記述タイプ: Other
• 論文抄録(英) / 内容記述: The amino acid sequence of a protein carries its folding information. If the information is encoded by the arrangement of the amino acid residues along the primary structure, the random shuffling of the residues would degrade the information. We developed a new method to compare the native sequence with random sequences generated from the native sequence, in order to extract such information. First, amino acid indices were randomly generated. That is, the initial indices have no significance on the feature of residues. Next, using the indices, the averaged distance between a native sequence and the random sequences was calculated, based on the autoregressive (AR) analysis and the linear predictive coding (LPC) cepstrum analysis. The indices were subjected to the genetic algorithm (GA) using the distance as the fitness, so that the distance between the native sequence and the random sequences becomes larger. We found that the indices converged to hydrophobicity indices by the GA operation. The AR analysis with the converged indices revealed that the autocorrelation in the native sequence is related to the secondary structure.
• 書誌レコードID / 収録物識別子タイプ: NCID
• 書誌レコードID / 収録物識別子: AA11464803
• 書誌情報: 情報処理学会論文誌数理モデル化と応用（TOM）; 巻 41, 号 SIG07(TOM3), p. 23-40, 発行日 2000-11-15
• ISSN / 収録物識別子タイプ: ISSN
• ISSN / 収録物識別子: 1882-7780
• 出版者 / 言語: ja
• 出版者: 情報処理学会