cosmo swMATH ID: 6106 Software Authors: Oliver Bembom, Fabian Gallusser, and Sandrine Dudoit Description: Supervised detection of conserved motifs in DNA sequences. 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. Homepage: http://www.bioconductor.org/packages/2.10/bioc/html/cosmo.html Dependencies: R Related Software: GASpAR; DUNE; MM5; ExnerFOAM; DYNAMICO; AROME; ALADIN-NH; ARPEGE; NICAM; MMesh3D; Fim; ASAM; Puma; EULAG; Isorropia; Alya; Scotch; Zoltan; PT-Scotch; p4est Cited in: 3 Publications Standard Articles 1 Publication describing the Software, including 1 Publication in zbMATH Year Supervised detection of conserved motifs in DNA sequences with cosmo. Zbl 1166.92304Bembom, Oliver; Keles, Sunduz; Van der Laan, Mark J. 2007 all top 5 Cited by 11 Authors 2 Giraldo, Francis X. 2 Kopera, Michal A. 1 Bembom, Oliver 1 Houzeaux, Guillaume 1 Jorba, Oriol 1 Keles, Sunduz 1 Kelly, James F. 1 Marras, Simone 1 Moragues, Margarida 1 Van der Laan, Mark Johannes 1 Vazquez, Mariano Cited in 3 Serials 1 Journal of Computational Physics 1 Archives of Computational Methods in Engineering 1 Statistical Applications in Genetics and Molecular Biology Cited in 5 Fields 2 Numerical analysis (65-XX) 2 Fluid mechanics (76-XX) 2 Geophysics (86-XX) 1 Statistics (62-XX) 1 Biology and other natural sciences (92-XX) Citations by Year