| BloodExpress | A
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. |
| Comodis | Extracts 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. |
| TFBScluster | Identifies 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. |
| TFBSsearch | Searches for potential TFBSs that are conserved throughout multiple aligned
sequences/a single sequence. Allows for feature masking. |
| SynPlot | Produces a visual representation of %identity between two or more sequences, in
.ps or .pdf format. Annotation features may also be plotted. |
| SynPlot-Peaks | Designed to work alongside SynPlot to identify the location of peaks of sequence
similarity above a specifiied value. |
| Peak Extractor | Extracts a specific region from an alignment, such as a peak of sequence identity from
SynPlot. |
| Block Counter | Displays and counts blocks of complete identity between two or more sequences.
Feature masking is also possible here. |
| Variable Width Bar Graph Drawer | Draws bar graphs with variable width vars. Useful for displaying ChIP/chip. |
| Perl scripts | The scripts of all the tools presented here. |
| Display TFBSsearch sites | A short tutorial. |
| Problems with any of the above | Please click here |
