Supervised detection of conserved motifs in DNA sequences with cosmo.

@article{Bembom2007SupervisedDO,
  title={Supervised detection of conserved motifs in DNA sequences with cosmo.},
  author={Oliver Bembom and S{\"u}nd{\"u}z Keles and Mark J van der Laan},
  journal={Statistical applications in genetics and molecular biology},
  year={2007},
  volume={6},
  pages={
          Article8
        }
}
A number of computational methods have been proposed for identifying transcription factor binding sites from a set of unaligned sequences that are thought to share the motif in question. We here introduce an algorithm, called cosmo, that allows this search to be supervised by specifying a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may be formulated, for example, on the basis of prior knowledge about the structure of the transcription… CONTINUE READING