NDLI: Iterative sequential Monte Carlo algorithm for motif discovery

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IET Wireless Sensor Systems

Micro & Nano Letters

The Journal of Engineering

Iterative sequential Monte Carlo algorithm for motif discovery

Content Provider	IET Digital Library
Author	Bataineh, Mohammad Al qudah, Zouhair Al Zaben, Awad Al
Abstract	The discovery of motifs in transcription factor binding sites is important in the transcription process, and is crucial for understanding the gene regulatory relationship and evolution history. Identifying weak motifs and reducing the effect of local optima, error propagation and computational complexity are still important, but challenging tasks for motif discovery. This study proposes an iterative sequential Monte Carlo (ISMC) motif discovery algorithm based on the position weight matrix and the Gibbs sampling model to locate conserved motifs in a given set of nucleotide sequences. Three sub-algorithms have been proposed. Algorithm 1 (see Fig. 1) deals with the case of one motif instance of fixed length in each nucleotide sequence. Furthermore, the proposed ISMC algorithm is extended to deal with more complex situations including unique motif of unknown length in Algorithm 2, unique motif with unknown abundance in Algorithm 3 (see Fig. 2) and multiple motifs. Experimental results over both synthetic and real datasets show that the proposed ISMC algorithm outperforms five other widely used motif discovery algorithms in terms of nucleotide and site-level sensitivity, nucleotide and site-level positive prediction value, nucleotide-level performance coefficient, nucleotide-level correlation coefficient and site-level average site performance.
Starting Page	504
Ending Page	513
Page Count	10
ISSN	17519675
Volume Number	10
e-ISSN	17519683
Issue Number	Issue 5, Jul (2016)
Alternate Webpage(s)	https://digital-library.theiet.org/content/journals/iet-spr/10/5
Alternate Webpage(s)	https://digital-library.theiet.org/content/journals/10.1049/iet-spr.2014.0356
Journal	IET Signal Processing
Publisher Date	2016-07-01
Access Restriction	Open
Rights Holder	© The Institution of Engineering and Technology
Subject Keyword	Biomedical Engineering Computational Complexity Evolution History Gene Regulatory Relationship Genetic Engineering Gibbs Sampling Model Interpolation And Function Approximation ISMC Algorithm Iterative Method Iterative Sequential Monte Carlo Algorithm Monte Carlo Method Motif Discovery Algorithm Nucleotide Sequence Nucleotide-level Correlation Coefficient Nucleotide-level Performance Coefficient Numerical Analysis Numerical Approximation And Analysis Position Weight Matrix Probability Theory Site-level Positive Prediction Value Statistics Stochastic Linearised SCUC Transcription Factor Binding Site
Content Type	Text
Resource Type	Article
Subject	Signal Processing Electrical and Electronic Engineering

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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