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PLOS Computational Biology: Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

Discovering TFBSs in…Repetitive Regions of #Genomes with Multi-Read
Analysis http://journals.PLOS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002111 CSEM uses EM to refine site occupancy

Chung D, Kuan PF, Li B, SanalKumar R, Liang K, Bresnick E, Dewey C, and Keles S (2011), “Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data,” PLoS Computational Biology, 7(7): e1002111

http://www.stat.wisc.edu/~keles/Software/multi-reads/

CSEM

https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=e18c78b20646a2aa&tool_config=database%2Fcommunity_files%2F000%2Frepo_83%2Fcsem.xml&changeset_revision=1438767ad92f

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