cosmo
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.
| Author |
Oliver Bembom, Fabian Gallusser, and Sandrine Dudoit |
| Maintainer |
Oliver Bembom |
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("cosmo")
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