Probability of occurrence of specific oligomers》.pdf

J. theor. Biol. (1992) 159, 299-306 Probability of Occurrence of Specific Oligomers ERIKA E. STOCKLE, PETER J. NIELSEN AND ULRICH GROBt Max-Ptanck-Institut fiir Immunbiologie, Stiibeweg 51, D-7800 Freiburg, Germany (Received on 6 December 1991, Accepted on 20 March 1992) We improved an already existing formula for calculating the probability of occur- rence of specific oligomers (Grob Stiiber, 1987) by taking into account unequal base distribution. This method identifies specific oligomers in a given sequence as candidates for biological signals. 1. Introduction Recently we have presented a model concerning statistical analysis of nucleic acid sequences (Stiickle et al., 1990). This model, however, is only applicable for long sequences or short oligomers where the expected occurrence of an oligomer in the test sequence is significantly greater than one. In this paper we are interested in methods of finding specific significant oligomers, even if the statistical model cannot be used. In this case, if the oligomers are too long or the sequences are too short to use the statistical model (Stiickle et al., 1990), one can ask for the probability that a specific oligomer occurs by chance in a given sequence. If this probability is small and the oligomer occurs often in the given sequence, it is a candidate for a biological signal. Von Hippel described the basic algorithm for assessing probability values of oligomers in nucleic acid sequences (Von Hippel, 1979). Later, exte