NDLI: GAPK: Genetic algorithms with prior knowledge for motif discovery in DNA sequences

Content Provider	IEEE Xplore Digital Library
Author	Dianhui Wang Xi Li
Copyright Year	2009
Description	Author affiliation: Department of Computer Science and Computer Engineering, La Trobe University, Melbourne, Victoria 3086, Australia (Dianhui Wang; Xi Li)
Abstract	Discovery of transcription factor binding sites (TFBSs) or DNA motifs in promoter regions of genes plays a key role in understanding the regulations of gene expression. In the past decade computational approaches, including evolutionary computation techniques, for searching for motifs have demonstrated good potential, and some results reported in literature are quite promising. Recently, some favorable progresses on evolutionary mining of motifs have been made and documented in GAME and GALF-P, where GAME employs a Bayesian-based scoring function and GALF-P aims to improve the algorithm performance with local filtering and adaptive post-processing. To improve discovering performance in terms of the recall, precision rates and algorithm reliability, this paper presents an alternative genetic algorithm termed as GAPK for resolving the problem of motifs discovery. In our proposed GAPK framework, a prior knowledge on motifs in a given dataset is used to initialize a population. Our technical contributions include a matrix representation for k-mers, a mismatch-based filtering method for search space reduction, a model mismatch score (MMS) as fitness function, new genetic operations and a model refinement processing. Some benchmarked datasets associated with eight transcription factors are used in our experiments. Comparative studies were carried out with well-known tools including GAME, GALF-P, MEME, MDScan and AlignACE. Results show that our method outperforms other techniques in terms of F-measure.
Starting Page	277
Ending Page	284
File Size	172645
Page Count	8
File Format	PDF
ISBN	9781424429585
DOI	10.1109/CEC.2009.4982959
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-05-18
Publisher Place	Norway
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Genetic algorithms DNA Sequences Gene expression Genomics Bioinformatics Filtering algorithms Problem-solving Computer science Data mining
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
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
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