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 palindrome conserved sequence
elements within an input enhancer CSC and then search a genomic CSC
database for other CSCs that share conserved sequence elements with the
input enhancer. 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 CSC. cis-Decoder searches a Drosophila CSC
database that consists of ~100,000 CSCs associated with >90% of the euchromatic
genome, including structural genes, 3'UTRs, flanking conserved sequences and
most previously identified enhancers.
 cis-Decoder Advanced Search (click here)
can be used to analyze CSCs from nematodes, mosquitoes, vertebrates or user generated custom CSC libraries from any phyla.
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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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