cDT-Cleaner

Generation of tissue specific cDT libraries is accomplished using readouts of the CSB-aligner and requires use of the JavaScript program cDT-cleaner. Making enhancer-type specific libraries requires two different CSB-libraries generated from functionally different enhancers, a library from the tissue of interest (e.g. neural), and a second library that serves as an 'out-group' (e.g. mesodermal). For the generation of a neural cDT-library, neural CSBs in both forward and reverse directions were copy/pasted into both upper and lower windows of CSB-aligner. The resulting cDTs from this alignment are listed in the 'Result of CSB alignment table' of the CSB-aligner output, in the column titled 'Motif.' Since this cDT list contains multiple copies of different cDTs, the extra copies are removed using the Java applet Puzzamatic 1.0 (a freeware created by Ron Surratt. The cDT list that contains all unique cDTs is then Alphabetized and sorted by size also using Puzzamatic 1.0. The cDTs, constituting a raw neural cDT-library, were then copy/pasted into a Microsoft Word document.

A second CSB-alignment is then performed with the neural CSBs in the top window of CSB-aligner, and mesodermal CSBs (both forward and reverse directions) in the lower window. The cDTs from this alignment were freed of extra copies as above. These cDTs constituted an unedited common neural/mesodermal cDT-library. The unedited neural and common cDT-libraries are combined and cDTs common to the two libraries (present in the first and second alignments) are both removed using cDT-cleaner, thus leaving only the neural-specific sequences.

cisDecoder
           Introduction
            CSB-aligner
            cDT-scanner
            cDT-cataloger