Net Nearest Neighbor Analysis (NNNA) summarizes non-compensated dinucleotides within gene sequences

Motivation: Net Nearest Neighbor Analysis (NNNA) measures a previously unex amined aspect of dinucleotide frequency-the non-compensated, non-repetitive dinucleotides in a sequence. Non-compensated dinucleotides are those in ex cess of their corresponding reverse dinucleotides, Results: NNNA regards dinucleotides as vector quantities, making it possibl e to summarize any sequence as a group of circuits and tags. The results of NNNA are found to be consistent with traditional analytic methods, yet rev eal additional characteristics of the sequences. The NNNA circuits and tags uniquely identify each tRNA in Escherichia coli K-12 and certain structura l components of each tRNA, extract function-specific characteristics for ea ch of the sequences involved in the formation of insulin from preinsulin, a nd exhibit species-specific phylogenetic characterization (demonstrated wit h Monilinia).