Analysis of large nucleic acid dot matrices on small computers

Abstract

A UCSD Pascal program was developed which can analyze nucleic acid dot matrices of up to 9500 X 9500 in size on the Apple II computer. Although matrices of such size consume large amounts of computer memory, this program minimizes these problems by analyzing only small strips of the matrix at a time, and then transferring the results to a floppy disk or printer. Compression and memory efficient code further enhance the size of the matrix that can be analyzed. By generating an image of the dot matrix using software, and sending this image directly to an Epson dot matrix printer, a very detailed print out may be produced. The program has a number of user selectable options which allow a great deal of control over the analysis. The program contains no computer dependent code, and thus should work on all systems that can run UCSD Pascal.