A Greedy Two-stage Gibbs Sampling Method for Motif Discovery in Biological Sequences

• Published in: Journal of Information Science and Engineering Vol. 26; no. 6; pp. 2309 - 2318
• Main Authors: 刘立芳(LI-FANG LIU), 焦李成(LI-CHENG JIAO)
• Format: Journal Article
• Language: English
• Published: Taipei 社團法人中華民國計算語言學學會 01.11.2010; Institute of Information Science, Academia sinica
• Subjects: Analytical, structural and metabolic biochemistry; Applied sciences; Biological and medical sciences; Computer science; control theory; systems; Computer systems and distributed systems. User interface; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; General aspects, investigation methods; Proteins; Software; binding sites; biological sequences; motif discovery; greedy motifSAM; Gibbs sampling; transcription factors; Scalability; Software package; DNA sequence; Binding site; Modeling; Protein; Sampler; Database; Knowledge discovery; Reliability; Pulse duration modulation; Bioinformatics
• ISSN: 1016-2364
• DOI: 10.6688/JISE.2010.26.6.23

For the motif discovery problem of DNA or protein sequences, a greedy two-stage Gibbs sampling algorithm is presented, and the related software package is called Greedy Motifsam. Based on position weight matrix (PWM) motif model, a greedy strategy for choosing the initial parameters of PWM is employed. Two sampling methods, site sampler and motif sampler, are used. Site sampler is used to find one occurrence per sequence of the motif in the dataset. Motif sampler is used to find zero or more non-overlapping occurrences of the motif in each sequence. The algorithm is capable of discovering several different motifs with differing numbers of occurrences in a single dataset. We use the binding sites (motif) information of eukaryotic transcription factors stored in TRANSFAC database to test our methods. The prediction accuracy, scalability and reliability are compared to several other methods. Our proposed method is also illustrated as applied to helix-turn-helix proteins, lipocalins, and prenyltransferases. The Greedy Motifsam software is available at http://lxy.xidian.edu.cn/math/intro/teachers/ qxg/MotifSAM.zip.