readme for ABaCUS v. 0.60 15 February 1995 A.S. ARCHIVE CONTENTS abacus.readme (this file-- guide to accompanying archive) abacus.tar.Z (compressed UNIX tape archive with makefile, sources, docs) abacus.zip (zipped DOS executable, sources, docs) abacus.hqx (bin-hexed self-extracting Mac app, sources, docs) Choose the archive that is right for you (Mac, DOS, UNIX). Each archive contains the source code, an extensive set of instructions, and sample data. The Mac and DOS archives also include pre-compiled programs. WHAT IS ABACUS? ABaCUS is a no-frills program developed to investigate the significance of the putative correspondence between exons and units of protein structure. This type of analysis takes the form of an attempt to eliminate the reference hypothesis (sometimes called a "null" hypothesis) that no correspondence exists. A reference hypothesis in this case consists of a reference model for random gene structures, and a scoring rule for quantifying correspondences. ABaCUS creates and reads files containing observed data supplied by the user, then uses this information to generate reference genes according to one of several available models. The observed and reference genes are then scored according to a correspondence rule designated by the user, and the scores are compared in order to determine whether the reference hypothesis (i.e., no correspondence) can be rejected. This program may be useful in your research if you are studying the origin and evolution of intron-containing genes. (end of readme file)