An efficient algorithm for deciphering regulatory motifs

DOI10.1007/978-1-84628-780-0_12MaRDI QIDQ5326189zbMATH OpenOpenAlexFDO

Authors Xiucheng Feng, Lin Wan, Minghua Deng, Fengzhu Sun, Minping Qian

Publication date 31 July 2013

Published in Networks: From Biology to Theory (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-1-84628-780-0_12

Mathematics Subject Classification ID

Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10)

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(13)

• Transcription factor binding sites detection by using alignment-based approach
• Efficient identification of transcription factor binding sites with a graph theoretic approach
• An efficient algorithm to identify DNA motifs
• A mathematical model in the study of genes for identifying transcription factor binding sites
• Identifying DNA motifs based on match and mismatch alignment information
• The p53MH algorithm and its application in detecting p53-responsive genes
• Finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross-species conservation
• Transcription factor-binding site identification and gene classification via fusion of the supervised-weighted discrete kernel clustering and support vector machine
• SegHMC: an algorithm for discovery of cis-regulatory module based on segmental HMM
• Identifying potential regulatory elements by transcription factor binding site alignment using partial order graphs
• Decoding transcriptional regulatory interactions
• Establishing a statistic model for recognition of steroid hormone response elements
• Detection of over-represented motifs corresponding to known TFBSs via motif clustering and matching

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Uses Software

• DWE
• BioProspector
• ClustalW
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