We would like to announce the release of cis-Decoder: BETA Version 1.1
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 suite of algorithms that scans input
CSCs, identified by the phylogenetic footprinting tool EvoPrinter
<http://evoprinter.ninds.nih.gov/> (http://evoprinter.ninds.nih.gov/), and
then searches a genomic CSC database for other related CSCs. CSC relatedness
is judged based on 1) repeat elements in the input CSC that are shared with
database CSCs and 2) elements that are uniquely shared between input and
database CSCs. 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 currently searches a Drosophila CSC database consisting of
~60,000 CSCs associated with ~1400 genes and their flanking regions,
encompassing ~60% of the Drosophila genome. Within the next six months we
hope to include all genomic CSCs in the database.
Because cis-Decoder 1.1 is a BETA version we ask for your feedback. Please
E-mail Tom Brody (brodyt from ninds.nih.gov) or Ward Odenwald
(ward from codon.nih.gov) with your comments.
Neural Cell-Fate Determinates Section
NINDS, NIH, Bethesda