The function of cis-Decoder tag scanner (cDT-scanner) is to determine the relationship between any one enhancer and any other group or groups of enhancers. cDT-scanner is used to align the cDTs contained within various cDT-libraries with conserved sequence blocks (CSBs) identified by EvoPrinter and curated by EvoPrint-parser.

Links to our cDT-libraries are given below:

• Drosophila cDT libraries
  • Drosophila neural cDTs
  • Drosophila mesodermal cDTs
  • Drosophila segmental cDTs
  • Drosophila common cDTs
• Mammalian cDT libraries
  • Mammalian neural cDTs
  • Mammalian mesodermal cDTs
  • Mammalian common cDTs
• Combined Drosophila/mammalian cDT libraries
  • neural cDTs
  • mesodermal cDTs

cDT-scanner is a Java applet that uses a variant of the CSB-aligner; it looks for only perfect matches between cDTs and CSB sequences. Alignment of cDTs using cDT-scanner is accomplished by pasting a cDT-library in the upper window of cDT-scanner and the EvoPrint or CSBs to which they are to be aligned in the lower window. The output of cDT-scanner consists perfect matches of cDTs aligned under the CSBs. Since each library consists of cDTs shared by different enhancers, cDT-aligner portrays the shared elements within each CSB. A cDT-scanner alignment should be saved; information from saved files can be copy-pasted into Microsoft Word. A second output window for the cDT-scanner, a results table, is a list of the aligned matches along with their positions. Each of the output columns of the results table can be sorted by selecting the column header of the column to be sorted. Contents of results tables can be copy-pasted into Microsoft Word. To make the readout appear as it does in the HTML file, do the following: 1) change the page orientation to horizontal (in the 'Page setup' option of the file menu of Word), 2) convert the font to Courier and 3) reduce the font size to 8.

An example of a cDT-scanner alignment is given below.

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.

Discover multispecies conserved sequences using EvoPrinter.