NDLI: Short adjacent repeat identification based on Chemical Reaction Optimization

Content Provider	IEEE Xplore Digital Library
Author	Jin Xu Lam, A.Y.S. Li, V.O.K. Qiwei Li Xiaodan Fan
Copyright Year	2012
Description	Author affiliation: Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, 94720, USA (Lam, A.Y.S.) \|\| Department of Statistics, The Chinese University of Hong Kong, Sha Tin, Hong Kong (Qiwei Li; Xiaodan Fan) \|\| Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong (Jin Xu; Li, V.O.K.)
Abstract	The analysis of short tandem repeats (STRs) in DNA sequences has become an attractive method for determining the genetic profile of an individual. Here we focus on a more general and practical issue named short adjacent repeats identification problem (SARIP), which is extended from STR by allowing short gaps between neighboring units. Presently, the best available solution to SARIP is BASARD, which uses Markov chain Monte Carlo algorithms to determine the posterior estimate. However, the computational complexity and the tendency to get stuck in a local mode lower the efficiency of BASARD and impede its wide application. In this paper, we prove that SARIP is NP-hard, and we also solve it with Chemical Reaction Optimization (CRO), a recently developed metaheuristic approach. CRO mimics the interactions of molecules in a chemical reaction and it can explore the solution space efficiently to find the optimal or near optimal solution(s). We test the CRO algorithm with both synthetic and real data, and compare its performance in mode searching with BASARD. Simulation results show that CRO enjoys dozens of times, or even a hundred times shorter computational time compared with BASARD. It is also demonstrated that CRO can obtain the global optima most of the time. Moreover, CRO is more stable in different runs, which is of great importance in practical use. Thus, CRO is by far the best method on SARIP.
Starting Page	1
Ending Page	8
File Size	1243099
Page Count	8
File Format	PDF
ISBN	9781467315104
e-ISBN	9781467315098
e-ISBN	9781467315081
DOI	10.1109/CEC.2012.6256614
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-06-10
Publisher Place	Australia
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Polynomials Chemicals Optimization DNA Vectors Silicon Tin maximum a posteriori Short adjacent repeats Chemical Reaction Optimization
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
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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7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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