ChIPmeta

Application data
Biological application domain(s)	Transcription Factor Binding Site identification, ChIP-Seq, ChIP-Chip
Principal bioinformatics method(s)	Hierarchical Hidden Markov Model
Maintained?	Maybe

Summary: Combining data from ChIP-seq and ChIP-chip.

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In HHMM, inference results from individual HMMs in ChIP-seq and ChIP-chip experiments are summarized by a higher level HMM. Simulation studies show the advantage of HHMM when data from both technologies co-exist. Analysis of two well-studied transcription factors, NRSF and CTCF, also suggests that HHMM yields improved TFBS identification in comparison to analyses using individual data sources or a simple merger of the two.