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Autoregressive and Iterative Hidden Markov Models for Periodicity Detection and Solenoid Structure Recognition in Protein Sequences

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Abstract—Traditional signal processing methods cannot detect interspersed repeats and generally cannot handle nonstationary signals. In this paper, we propose a new method for periodicity detection in protein sequences to locate interspersed repeats. We first apply the autoregressive model with a sliding window to find possible repeating subsequences within a protein sequence. Then, we utilize an iterative hidden Markov model (HMM) to count the number of subsequences similar to each of the possible repeating subsequences. An iterative HMM search of the potential repeating subsequences can help identify interspersed repeats. Finally, the numbers of repeating subsequences are aggregated together as a feature and used in the classification process. Experiment results show that our method improves the performance of solenoid protein recognition substantially.

Index Terms—Autoregressive (AR) model, feature extraction, Markov model, solenoid protein recognition, spectral analysis.

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Ketersediaan

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Informasi Detail

Judul Seri

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No. Panggil

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Penerbit

: IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS., 2013

Deskripsi Fisik

IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS, VOL. 17, NO. 2, MARCH 2013 p. 436-441

Bahasa

English

ISBN/ISSN

2168-2194

Klasifikasi

NONE

Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

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Subjek

ANALISIS SPEKTRUM

Info Detail Spesifik

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Pernyataan Tanggungjawab

Nancy Yu Song, and Hong Yan

Versi lain/terkait

Lampiran Berkas

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