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Local Motif Finder LocaMo Finder

Detects regulatory motifs based on their local over-representation in sets of regulatory regions. LocaMo Finder is based on a non-parametric approach for sample density estimation, with adjustments which allow it to detect sequence regions that have a significant local enrichment in transcription factors, on a 1 bp resolution. It uses a Parzen window-based approach for scoring local enrichment, and during evaluation of significance it takes into account gene conversion content of sequences.

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LocaMo Finder classification

LocaMo Finder specifications

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Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Laboratory of Host Defense, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan

Funding source(s)

This work was supported by the Special Coordination Funds of the Japanese Ministry of Education, Culture, Sports, Science and Technology, and the Ministry of Health, Labour and Welfare in Japan, the Japan Society for the Promotion of Science through Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program), and by a Kakenhi Grant-in-Aid for Scientific Research (23710234) from the Japan Society for the Promotion of Science.

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