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.
 Mouse 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.
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Last updated on: September 8, 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.
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