Abstract
Many of protein binding sites in DNA are those by transcription factors (TFa). And the identification of these TFBSs in DNA sequences is very important for further understanding of underlying gene regulatory networks. When a set of regulatory regions of co-regulated genes are compared, only the significant appearance of similar short segments is observed and this motivates the development of specialized motif-finding (or motif-discovery) algorithms (instead pf conventional sequence aligners). Although a number of algorithms have been developed, the inherent problem of many false-positives has remained. With the progress of the ChIP-seq technology, requirements for these algorithms have been modulated. Anyway, we still need more research for better understanding of transcriptional regulatory mechanisms.
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