A COMBINATORIAL ALGORITHM FOR HIGHLY SPECIFIC RECOGNITION OF PROTEIN-CODING REGIONS IN HIGHER EUKARYOTIC DNA-SEQUENCES

We present a combinatorial algorithm for recognizing protein-ceding re gions in DNA sequences of higher eukaryotes. The developed algorithm p rovides highly specific recognition of protein-coding segments and is intended to be used in construction of oligonucleotide probes and PCR primers for analysis of cDNA libraries or total cell RNA. As distinct from other methods, this one is based on simple statistical indices (c odon usage and positional nucleotide frequencies at splicing sites) an d hence is applicable to obscure genomes, when large training samples are unavailable. The algorithm structure allows the researcher to read ily adapt it for various experimental requirements.