Staden: Statistical and Structural Analysis of Nucleotide Sequences

This chapter deals with performing simple statistical and structural analysis of nucleotide sequences, and also describes some more unusual tests. Base, dinucleotide and codon compositions, potential amino acid compositions, and the relative frequencies of each base in each position of codons are covered. This chapter describes how to produce plots to show regions of unusual composition and to measure the codon bias for a gene. In addition, it describes a set of functions for finding “structures” in nucleotide sequences, including short-range inverted repeats or stem-loops, long-range inverted repeats, long-range direct repeats, and Z DNA. AU the methods are contained in the program NIP.