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 Database consists of 348,567 computationally curated CSCs
with sequences that have been conserved for at least 400 million cumulative evolutionary divergent (CED) years. We are now generating a 1 billion CED year CSC database and expect that ~30% of
the CSCs in the 400 million year database will have sequences that have been conserved for more than 1 billion CED years. The search page will have updates concerning the number of
chromosomes that are currently in the 1 billion CED year database. See description of the database (click here).
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: April 23, 2013
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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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