CREAD (Comprehensive Regulatory Element Analysis & Discovery) includes efficient tools for performing fundamental tasks in motif discovery and regulatory sequence analysis. CREAD also includes code libraries to facilitate the implementation of new tools. In addition to fundamental tools, CREAD includes an implementation of the MARS machine learning algorithm, and a Suffix Tree implementation designed for repeated searching of large amounts of sequence data using position-weight matrices, a common representation for transcription-factor binding-sites.
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Citation:Andrew D. Smith, Pavel Sumazin, Zhenyu Xuan, and Michael Q. Zhang
DNA motifs in human and mouse proximal promoters predict tissue specific expression.
PNAS, 103(16):6275-6280 (2006) PDF Andrew D. Smith, Pavel Sumazin, Debopriya Das, and Michael Q. Zhang
Mining ChIP-chip data for transcription factor and cofactor binding sites.
Bioinformatics, 21(Suppl 1):i403–i412 (2005) PDF Dustin E. Schones, Pavel Sumazin, Michael Q. Zhang
Similarity of position frequency matrices for transcription factor binding sites.
Bioinformatics, 21(3):307-313 (2005) PDF