CisFinder: Identification of DNA over-represented motifs
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Description of CisFinder

CisFinder is a tool for finding over-representing short DNA motifs (e.g., transcription factor binding motifs) and estimates the Position Frequency Matrix (PFM) directly from word counts. It is designed for the analysis of ChIP-chip and ChIP-seq data and can process long input files (50 Mb). Identification and clustering of motifs takes 8 sec per 1 Mb. Other features: uses False discovery rate (FDR) and control sequences, finds motifs based on PFM.

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Sharov, A.A. and Ko, M.S.H. (2009). Exhaustive search for over-represented DNA sequence motifs with CisFinder. DNA Research, doi: 10.1093/dnares/dsp014.

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