TFBSfinder is a TFBS (transcription factor binding sites) identification method that utilizes several data sources, including DNA sequences, phylogenetic information, microarray data and ChIP-chip data. For a TF, TFBSfinder rigorously selects a set of reliable target genes and a set of non-target genes to find over-represented and conserved motifs in target genes. A new metric for measuring the degree of conservation at a binding site across species and methods for clustering motifs and for inferring position weight matrices are proposed. For synthetic data and yeast cell cycle TFs, TFBSfinder identifies motifs that are highly similar to known consensuses. Moreover, TFBSfinder outperforms well-known methods.
BIO-IT Station, Academia Sinica, Taiwan
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Bioinformatics. 2006 Jul 15;22(14):1675-81. Epub 2006 Apr 27.
Method for identifying transcription factor binding sites in yeast.
Tsai HK, Huang GT, Chou MY, Lu HH, Li WH.