We provide a menu-driven integration of the genetic programs of the Genetics Computer Group (GCG). This allows in-experienced users a very simple access to all GCG programs regardless of the system environment. No modifications to the GCG package are necessary.

COOL is a program designed to find COmmon OLigomers in a number of nucleic acid sequences. The results of COOL serve as starting points in sequence analysis investigations as well as suggestions for polymerase chain reaction probes. As an example we analyzed thyroid hormone receptor genes and found two oligomers which are characteristic of almost all those genes.

A set of programs has been developed for the definition and handling of nucleic acid sequence consensus information. The sequences of known genetic control signals are combined in a matrix. The origins and positions of the signals are recorded. Old matrices can be updated dynamically: new signals are included and obsolete ones deleted. Matrices of several different types are computed optionally. Several of these matrices can be combined to find possible new signals. The use of matrices allows the exact quantification of signal qualities. The described programs are part of a program library named GENEXPERT. Application examples given are the search for tRNA genes and the search for promoters in the bacteriophage lambda genome.

A program system for nucleic acid sequence analysis has been developed. The detection and prediction of secondary structures in nucleic acids have been especially emphasized. The system is able to handle most of the common problems found with nucleic acid sequencing like testing homologies, searching for reading frames and signals etc., but in addition it is able to locate and predict secondary structures. The predicted structures can either be printed on normal line printers or displayed on drawing devices like plotters or video screens. Another special feature is the data base-like handling of consensus sequence matrices by the programs DYCOM and EAGLE. Detailed descriptions of the programs have been published elsewhere (Stüber, 1985, 1986).