SeqSite is an efficient and easy-to-use software tool implementing a novel method for identifying and pinpointing 
transcription factor binding sites. It first detects transcription factor binding regions by clustering tags and statistical hypothesis testing, and locates every binding site in detected binding regions by modeling the tag profiles. It can pinpoint closely spaced adjacent binding sites from ChIP-seq data. This software is coded in C/C++, and supports major computer platforms.
Reference:
SeqSite, which can pinpoint both closely spaced and isolated binding sites, and consequently improves the resolution of TFBS detection from ChIP-seq data. BMC Systems Biology, 5(Suppl 2):S3.
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