Nearest-neighbor sequence analysis

Nearest neighbor analysis. A technique developed by Komberg and associates before the availability of sequencing methods is the nearest neighbor sequence... 

Nearest-neighbor effects refer to the reciprocal influence of adjacent amino acids on protein folding. In some cases, this term also refers to amino acids that are close in the 3-D structure of the protein (<8-10 A away), but distant in the sequence. Early studies found a nonrandom assorting of amino acids in secondary structures by pair-wise analysis of protein sequences (43). More recently, it was reported that the preference of pairs of amino acids for secondary structure was determined, in part. 

The next step in the description of the DNA sequence is the analysis of the pair-wise nearest-neighbor correlations Cy, for example, the normalized probabilities to And successive pairs of the nucleotides i and j. Eor all 16 possible successive dinucleotides in the coding strand of DNA, only the functions Cag and CcT correlate with OGT. The excess probabilities to find ApG and CpT pairs in the coding DNA are increasing significantly with OGT, correlation coefficient R = 0.68 and 0.601 (Fig. 2, upper row). Remarkably, the codon bias explains the observed sequence correlations in the coding parts of DNA. Eirst,... 

Fig. 2. Nearest-neighbor tree for SaPI core genomes. Lineups were determined and trees calculated by CLUSTAL analysis using VectorNti or MegAlign. Accessory genes were removed from the sequences used for this alignment so as to obtain an accurate view of the relationships among the basic SaPI genomes.

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