Run cDT-Cataloger

cDT-cataloger prepares a list of enhancer CSBs that contain shared sequence elements identified by the cis-Decoder tags (cDTs). cDT-cataloger is a Java applet that uses a variant of the cis-Decoder aligner; it looks for only perfect matches between cDTs of a specified size and CSB sequences. The output lists those enhancers containing sequences that match the cDTs tested. Cataloguing is accomplished by copy-pasting into the cDT-cataloger CSBs (both forward and reverse direction) in the upper window, and selected cDTs of a single size in the lower window. The size of the cDTs being catalogued must be typed into the box underneath the lower window.

A example of a cDT-cataloger readout is shown below. Eight cDTs and their alignment with CSBs are shown. For example, the cDT CTGGTG is designated mam_n3;m0-CTGGTG, indicating that it is a mammalian cDT that aligns with three CSBs of a mammalian neural CSB-library and does not align with CSBs of a mesodermal CSB-library. The three hits of CTGGTG on neural CSBs are aligned below the cDT; the first is a hit on the math1 enhancer CSB#30 in the forward direction.

Please feel free to contact Dr. Thomas Brody at brodyt@ninds.nih.gov or Dr. Ward Odenwald at odenwaldw@ninds.nih.gov if you have any questions about EvoPrinter or its applications.

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