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Short description:
Please summarise the application in a few sentences. Avoid links here. Combining data from ChIP-seq and ChIP-chip.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Transcription factors and regulatory sites, ChIP-seq, ChIP-on-chip,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Peak calling,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Command line
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
Command-line tool,
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.
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