RNA Dotplot

RNA Dotplot is a simple utility to print a dot matrix of the potential base pairing interactions in an RNA sequence.  The idea for this type of plot is quite old, but since I could not find a program to do it on my Macintosh, I wrote one.  The input file for the program MUST be a text only file containing the sequence (less than 130 bases) on a single line.   Because my programming abilities are limited, this was written and compiled with MicroSoftª QuickBasic.  Thus, the program is limited to input files containing 130 bases or less, and is rather slow.    Potential pairing between bases i and j in a sequence are indicated by a 1 for a G-U pair, a 2 for an A-U pair, and a 3 for a G-C pair, while the inability of bases i and j to form a GU, AU, or GC base pair is indicated by a dot.   Potential helices may be identified by looking for diagonal runs of numbers.  Output files should be viewed using a constant spaced font (i.e. courier).  A minimum helix length (1-3 bp) may be specified to clean-up the appearance of the output file, although very short base pairing interactions may be lost.  Although gaps or dashes are permitted in the input sequence, when a minimum helix lenght of 2 or 3 is selected, potential helices cannot cross gaps in the sequence.  

If you have any comments on the program, please let me know.

David S. McPheeters
mcpheeters@biochemistry.cwru.edu
September 1994