ccosmo: A stand-along C program for the supervised detection of conserved motifs in DNA sequences.(2006)
Abstractcosmo 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 DateMarch, 2006
Citation InformationO. 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).