Introduction: Analysis of cis-regulatory modules or enhancers reveals that they contain clusters of evolutionarily conserved sequences we refer to as conserved sequence clusters (CSCs). These CSCs are made up of multiple Conserved Sequence Blocks (CSBs). cis-Decoder is a suite of alignment programs that identify repeat and palindromic conserved sequence elements within an input enhancer and then searches a genomic database for other CSCs that share sequence elements with the input CSC. Conserved sequences within the input enhancer are first identified by the phylogenetic footprinting tool EvoPrinter. The CSCs identified in this search are candidates for enhancers that drive expression of an associated gene in the same or similar pattern to that obtained from the input cluster.

New Link Seach Mouse Genome CSC DatabaseMouse Genome CSC Databases represent four different levels of cumulative evolutionary conservation (400 My, 600 My, 1.0 By and 1.8 By). These libraries consist of 349,033 (400 My), 196,161 (600 My), 74,673 (1.0 By) and 7,821 (1.8 By) CSCs, including non-coding, coding and 3’UTR sequences. Both the 600 My and 1.0 By CSCs have been named by gene association, location and/or if available, with their literature designation. As of this date, many of the cluster names are unique to individual databases. To identify the genomic location of a database CSC, use the link on the CSC results alignment page or use of the eBLAT function available as a link on the left hand menu located on the input page. A full guide to use of cis-Decoder search algorithms for enhancer discovery and sequence analysis is given at the following site: cis-Decoder Tutorial

Drosophila Genome CSC Database consists of ~100,000 manually curated CSCs associated with >90% of the of the euchromatic genome.

cis-Decoder Advanced Search can be used with custom CSC libraries from any phylum (click here).

To initiate a search of the mouse or Drosophila CSC databases, first prepare an EvoPrint of your enhancer and then enter cis-Decoder.
Last updated on: April 1, 2014
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The cis-Decoder system and algorithms were developed by Amarendra S. Yavatkar, Leonard Tyson, Thomas Brody and Ward F. Odenwald of the National Institute of Neurological Disorders and Stroke, NIH. This site is maintained and hosted by NINDS, NIH, Bethesda MD.