Fuzzy profile hidden Markov models for protein sequence analysis

N. P. Bidargaddi, M. Chetty, J. Kamruzzaman

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Citation (Scopus)

Abstract

Profile HMMs based on classical hidden Markov models have been widely applied for alignment and classification of protein sequence families. The formulation of the forward and backward variables in profile HMMs is made under statistical independence assumption of the probability theory. We propose a fuzzy profile hidden Markov model to overcome the limitations of the statistical independence assumption of probability theory. The strong correlations and the sequence preference involved in the protein structures make fuzzy architecture based models as suitable candidates for building profiles of a given family since fuzzy set can handle uncertainties better than classical methods. The proposed model fuzzifies the forward and backward variables by Incorporating Sugeno fuzzy measures using Choquet integrals which is extended to fuzzy Baum-Welch parameter estimation algorithm for profiles. It was built and tested on widely studied globin and kinase family sequences and its performance was compared with classical HMM. A comparative analysis based on Log-Likelihood (LL) scores of sequences and Receiver Operating Characteristic (ROC) demonstrates the superiority of fuzzy profile HMMs over the classical profile model.

Original languageEnglish
Title of host publicationProceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05
PublisherIEEE Computer Society
ISBN (Print)0780393872, 9780780393875
DOIs
Publication statusPublished - Nov 2005
Externally publishedYes
Event2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05 - La Jolla, CA, United States
Duration: 14 Nov 200515 Nov 2005

Publication series

NameProceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05
Volume2005

Conference

Conference2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05
CountryUnited States
CityLa Jolla, CA
Period14/11/0515/11/05

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