CLARE: Cracking the LAnguage of Regulatory Elements

0301 basic medicine 0206 medical engineering Genomics 02 engineering and technology Regulatory Sequences, Nucleic Acid Mice 03 medical and health sciences Enhancer Elements, Genetic Prosencephalon Gene Expression Regulation Organ Specificity Animals Humans Software Transcription Factors
DOI: 10.1093/bioinformatics/btr704 Publication Date: 2011-12-24T02:37:52Z
ABSTRACT
AbstractSummary:  CLARE is a computational method designed to reveal sequence encryption of tissue-specific regulatory elements. Starting with a set of regulatory elements known to be active in a particular tissue/process, it learns the sequence code of the input set and builds a predictive model from features specific to those elements. The resulting model can then be applied to user-supplied genomic regions to identify novel candidate regulatory elements. CLARE's model also provides a detailed analysis of transcription factors that most likely bind to the elements, making it an invaluable tool for understanding mechanisms of tissue-specific gene regulation.Availability: CLARE is freely accessible at http://clare.dcode.org/.Contact:  taherl@ncbi.nlm.nih.gov; ovcharen@nih.govSupplementary information:  Supplementary data are available at Bioinformatics online.
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