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Presentation
ccosmo: A stand-along C program for the supervised detection of conserved motifs in DNA sequences.
(2006)
  • Oliver Bembom, University of California, Berkeley
  • Sunduz Keles
  • Mark Johannes van der Laan
Abstract
cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively.
Publication Date
March, 2006
Citation Information
O. Bembom, S. Keles, and M.J. van der Laan. ccosmo: A stand-along C program for the supervised detection of conserved motifs in DNA sequences (http://cosmoweb.berkeley.edu/software.html).