MISCORE: Mismatch-Based Matrix Similarity Scores for DNA Motif Detection

Wang, Dianhui and Lee, Nung Kion (2009) MISCORE: Mismatch-Based Matrix Similarity Scores for DNA Motif Detection. In: Advances in Neuro-Information Processing. Lecture Notes in Computer Science, 5506 . Springer Berlin/Heidelberg, pp. 478-485. ISBN 978-3-642-02490-0


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To detect or discover motifs in DNA sequences, two important concepts related to existing computational approaches are motif model and similarity score. One of motif models, represented by a position frequency matrix (PFM), has been widely employed to search for putative motifs. Detection and discovery of motifs can be done by comparing kmers with a motif model, or clustering kmers according to some criteria. In the past, information content based similarity scores have been widely used in searching tools. In this paper, we present a mismatchbased matrix similarity score (namely, MISCORE) for motif searching and discovering purpose. The proposed MISCORE can be biologically interpreted as an evolutionary metric for predicting a kmer as a motif member or not. Weighting factors, which are meaningful for biological data mining practice, are introduced in the MISCORE. The effectiveness of the MISCORE is investigated through exploring its separability, recognizability and robustness. Three well-known information contentbased matrix similarity scores are compared, and results show that our MISCORE works well.

Item Type: Book Chapter
Uncontrolled Keywords: Mismatchbased matrix similarity score, MISCORE, DNA, unimas, university, universiti, Borneo, Malaysia, Sarawak, Kuching, Samarahan, ipta, education, research, Universiti Malaysia Sarawak
Subjects: Q Science > QA Mathematics
T Technology > T Technology (General)
Divisions: Academic Faculties, Institutes and Centres > Faculty of Cognitive Sciences and Human Development
Depositing User: Karen Kornalius
Date Deposited: 12 May 2016 04:03
Last Modified: 12 May 2016 04:03
URI: http://ir.unimas.my/id/eprint/11923

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