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eCIS-ANALYST searches the Drosophila melanogaster and Drosophila pseudoobscura genomes for conserved clusters of transcription-factor binding sites.

An earlier version, CIS-ANALYST, allowed searches of the D. melanogaster genome for high-density clusters of predicted binding-sites for any combination of transciption factors with known binding specificity. We and others showed that this was a productive method for identifying functional developmental enhancers.

We recently completed functional tests of 37 predicted targets of BCD, HB, KR, KNI and CAD, showing that 15 function as anterior-posterior enhancers. We also showed that requiring that clusters found in D. melanogaster also be present in D. pseudoobscura greatly improved the accuracy of these predictions.


Berman BP*, Pfeiffer BD*, et. al. (2004). Genome Biol. 5:R61
[PDF | article @ Genome Biol. | web companion]

Berman BP, et. al. (2002). Proc. Natl. Acad. Sci. 99, 757-762
[PDF | article @ PNAS | commentary @ PNAS | web companion]