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We describe an interactive computer program (ANALYSEQ) that is used from a simple graphics terminal. The main purpose of the program is to determine the function of nucleic acid sequences but it also offers the simpler listing, searching and counting options. It contains methods to locate genes by looking for the effects that coding for a protein has on the coding sequence, to locate tRNA genes by looking for secondary structure and conserved bases, and methods to locate signals such as promoters. Techniques to identify unusual regions of sequence and to search for potential Z DNA-forming regions are also included. Most of the routines produce graphical output which gives ease of interpretation and allows superposition of several independent forms of analysis.
Rodger Staden (Sun,) studied this question.