has specified data input has specified data output implements has format specification is published by is executed in Image FASTA format R data frame cosmo Nandini Badarinarayan http://bioconductor.org/packages/2.4/bioc/html/cosmo.html 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. gene expression analysis HTML report BioConductor Software R software Cosmo Bioconductor