We consider the problem of predicting cis-regulatory modules without knowledge of motifs. We formulate this problem in a pragmatic setting, and create over 30 new data sets, using Drosophila modules, to use as a 'benchmark'. We propose two new methods for the problem, and evaluate these, as well as two existing methods, on our benchmark. We find that the challenge of predicting cis-regulatory modules ab initio, without any input of relevant motifs, is a realizable goal.
|Original language||English (US)|
|State||Published - Jan 28 2008|
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Cell Biology