A Generalized Hidden Markov Model Approach to Transmembrane Region Prediction with Poisson Distribution as State Duration Probabilities

• Item type: Trans(1)
• 公開日: 2008-03-15
• タイトル: A Generalized Hidden Markov Model Approach to Transmembrane Region Prediction with Poisson Distribution as State Duration Probabilities
• タイトル / 言語: en
• タイトル: A Generalized Hidden Markov Model Approach to Transmembrane Region Prediction with Poisson Distribution as State Duration Probabilities
• 言語: eng
• キーワード / 主題Scheme: Other
• キーワード / 主題: Original Papers
• 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: Waseda University
• 著者所属: Waseda University
• 著者所属(英): en
• 著者所属(英): Waseda University
• 著者所属(英): en
• 著者所属(英): Waseda University
• 著者名: Takashi, Kaburagi; Takashi, Matsumoto
• 著者名(英): Takashi, Kaburagi; Takashi, Matsumoto
• 論文抄録 / 内容記述タイプ: Other
• 論文抄録 / 内容記述: We present a novel algorithm to predict transmembrane regions from a primary amino acid sequence. Previous studies have shown that the Hidden Markov Model (HMM) is one of the powerful tools known to predict transmembrane regions; however one of the conceptual drawbacks of the standard HMM is the fact that the state duration i.e. the duration for which the hidden dynamics remains in a particular state follows the geometric distribution. Real data however does not always indicate such a geometric distribution. The proposed algorithm utilizes a Generalized Hidden Markov Model (GHMM) an extension of the HMM to cope with this problem. In the GHMM the state duration probability can be any discrete distribution including a geometric distribution. The proposed algorithm employs a state duration probability based on a Poisson distribution. We consider the two-dimensional vector trajectory consisting of hydropathy index and charge associated with amino acids instead of the 20 letter symbol sequences. Also a Monte Carlo method (Forward/Backward Sampling method) is adopted for the transmembrane region prediction step. Prediction accuracies using publicly available data sets show that the proposed algorithm yields reasonably good results when compared against some existing algorithms.
• 論文抄録(英) / 内容記述タイプ: Other
• 論文抄録(英) / 内容記述: We present a novel algorithm to predict transmembrane regions from a primary amino acid sequence. Previous studies have shown that the Hidden Markov Model (HMM) is one of the powerful tools known to predict transmembrane regions; however, one of the conceptual drawbacks of the standard HMM is the fact that the state duration, i.e., the duration for which the hidden dynamics remains in a particular state follows the geometric distribution. Real data, however, does not always indicate such a geometric distribution. The proposed algorithm utilizes a Generalized Hidden Markov Model (GHMM), an extension of the HMM, to cope with this problem. In the GHMM, the state duration probability can be any discrete distribution, including a geometric distribution. The proposed algorithm employs a state duration probability based on a Poisson distribution. We consider the two-dimensional vector trajectory consisting of hydropathy index and charge associated with amino acids, instead of the 20 letter symbol sequences. Also a Monte Carlo method (Forward/Backward Sampling method) is adopted for the transmembrane region prediction step. Prediction accuracies using publicly available data sets show that the proposed algorithm yields reasonably good results when compared against some existing algorithms.
• 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: AA12177013
• 書誌情報: IPSJ Transactions on Bioinformatics （TBIO）; 巻 49, 号 SIG5(TBIO4), p. 1-14, 発行日 2008-03-15
• ISSN / 収録物識別子タイプ: ISSN
• ISSN / 収録物識別子: 1882-6679
• 出版者 / 言語: ja
• 出版者: 情報処理学会