Sitesifter
SiteSifter finds highly conserved DNA motifs embedded within coding
regions. Each instance of a motif is scored based on the chance that
its constituent codons are conserved over and above that required for
amino acid conservation.
Software Paper
COALESCE
COALESCE uses large collections of genomic data and Bayesian
integration to predict coregulated gene modules, the conditions of
regulation, and the consensus binding motifs for regulation. It uses
a synthesis of gene expression biclustering, motif prediction, and
data integration (including expression, sequence, nucleosome
positioning, and evolutionary conservation). It is available as part
of the Sleipnir library.
Software Paper
Nearest Neighbor Networks
Nearest Neighbor Networks (NNN) is a graph-based algorithm used to
cluster genes with similar microarray expression profiles. The NNN
clustering method is an alternative to classical techniques such as
hierarchical and K-means clustering. NNN generates clusters of
functionally related genes with high precision, and the clusters
generally represent a broader selection of biological processes than
those produced by other methods; NNN performs best on data sets with
many conditions and on datasets that are modular (i.e. contain several
grouped subsets of conditions).
Software Paper