scholarly journals Classification of the Adenylation and Acyl-Transferase Activity of NRPS and PKS Systems Using Ensembles of Substrate Specific Hidden Markov Models

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e62136 ◽  
Author(s):  
Barzan I. Khayatt ◽  
Lex Overmars ◽  
Roland J. Siezen ◽  
Christof Francke
Keyword(s):  
Hidden Markov Models ◽  
Markov Models ◽  
Hidden Markov ◽  
Transferase Activity ◽  
Acyl Transferase ◽  
Acyl Transferase Activity

scholarly journals CutProtFam-Pred: Detection and classification of putative structural cuticular proteins from sequence alone, based on profile Hidden Markov Models

2014 ◽  
Vol 52 ◽  
pp. 51-59 ◽  
Author(s):  
Zoi S. Ioannidou ◽  
Margarita C. Theodoropoulou ◽  
Nikos C. Papandreou ◽  
Judith H. Willis ◽  
Stavros J. Hamodrakas
Keyword(s):  
Hidden Markov Models ◽  
Markov Models ◽  
Hidden Markov ◽  
Profile Hidden Markov Models ◽  
Cuticular Proteins

scholarly journals Sequence Classification Using Third-Order Moments

2018 ◽  
Vol 30 (1) ◽  
pp. 216-236
Author(s):  
Rasmus Troelsgaard ◽  
Lars Kai Hansen
Keyword(s):  
Hidden Markov Models ◽  
Markov Models ◽  
Sequence Data ◽  
Hidden Markov ◽  
Score Function ◽  
Simulated Data ◽  
Discrete Observations ◽  
Third Order ◽  
Leibler Divergence

Model-based classification of sequence data using a set of hidden Markov models is a well-known technique. The involved score function, which is often based on the class-conditional likelihood, can, however, be computationally demanding, especially for long data sequences. Inspired by recent theoretical advances in spectral learning of hidden Markov models, we propose a score function based on third-order moments. In particular, we propose to use the Kullback-Leibler divergence between theoretical and empirical third-order moments for classification of sequence data with discrete observations. The proposed method provides lower computational complexity at classification time than the usual likelihood-based methods. In order to demonstrate the properties of the proposed method, we perform classification of both simulated data and empirical data from a human activity recognition study.

scholarly journals Classification of HIV-1 Sequences Using Profile Hidden Markov Models

PLoS ONE ◽  
2012 ◽  
Vol 7 (5) ◽  
pp. e36566 ◽  
Author(s):  
Sanjiv K. Dwivedi ◽  
Supratim Sengupta
Keyword(s):  
Hidden Markov Models ◽  
Markov Models ◽  
Hidden Markov ◽  
Profile Hidden Markov Models ◽  
Hiv 1
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