Software from the HSCL (links to older site)

BloodExpressA database of gene expression in mouse blood stem cells--you can query by gene name, or extract lists of genes expressed in specific blood cell types.
ComodisExtracts regions of sequence surrounding conserved TFBSs of your choice (seed motifs) within a given distance of a set of coregulated genes.  The output can be used for novel motif discovery.
HAEMCODEA comprehensive functional genomic data compendium for mouse haematopoiesis based on publicly available datasets.
TFBSclusterIdentifies clusters of TFBSs throughout the human or mouse genomes that are conserved in multiple mammalian species.
TFBScluster (user-supplied alignment)Same as above but the user supplies the multiple alignment.
TFBSsearchSearches for potential TFBSs that are conserved throughout multiple aligned sequences/a single sequence.  Allows for feature masking.
SynPlotProduces a visual representation of %identity between two or more sequences, in .ps or .pdf format.  Annotation features may also be plotted.
SynPlot-PeaksDesigned to work alongside SynPlot to identify the location of peaks of sequence similarity above a specifiied value.
Peak ExtractorExtracts a specific region from an alignment, such as a peak of sequence identity from SynPlot.
Block CounterDisplays and counts blocks of complete identity between two or more sequences.  Feature masking is also possible here.
Variable Width Bar Graph DrawerDraws bar graphs with variable width vars.  Useful for displaying ChIP/chip.
Perl scriptsThe scripts of all the tools presented here.
Display TFBSsearch sitesA short tutorial.
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