Linguistic analysis of nucleotide sequences: Algorithms fdr pattern recognition and analysis of codon strategy

The linguistic approach to the analysis of nucleotide sequences reveals a powerful tool for a number of purposes, including the identification of sequence motifs having a functional role, the establishment of functional correlations between strings, and the study of phylogenetic relationships between genetic texts (i.e., evolutionary analyses). Linguistic approaches to the analysis of genetic material are numerous and differ according to the particular goal of the study. This chapter presents a short introduction to the commonest aspects and treatments of nucleotide sequences as a language and two algorithms of linguistic analysis. The algorithm WORDUP is aimed at the identification of statistically significant oligonucleotide motifs. Such a method is, particularly suitable to the analysis of a huge number of sequences having unknown functions produced by automatic sequencing procedures. The algorithm CODONTREE is aimed at the study of codon strategy in protein coding genes