Codon Usage And Comparison In Synonymous Codon Repeats Sequences

In the first part, based on the synonymous codon repeat sequences of E.coli coding sequences, the difference of codon usage is analyzed between synonymous codon repeat sequences and all coding sequences. Compared with all of the coding sequences, we find that the codon usage has distinct difference for some codons in synonymous codon repeat sequences; the same codon repeats have the position bias in 4 synonymous codon repeat segments; some codons' usage is correlated with the gene expression levels in synonymous codon repeat segments.In the second part: based on the amino acid sequences which translated by coding sequence in six genomes, which are Archaeoglobus fulgidus Bacillus subtilis Escherichia coli Saccharomyces cerevisiae Caenorhabditis elegans andArabidopsis thaliana, the amino acid usage in amino acid repeat sequences is discussed. The distribution of amino acid repeat segment numbers with its repeat lengh is given. We find that the distributions are correlated with genome evolution and the amino acid content is changed with the amino acid repeat lengh. Furthermore, we find that the maximum lenghs of amino acid repeat are affected by the hydrophobicity and hydrophilicity and amino acid volume as well as the polarity of amino acid.In the third part, by using the coding sequences of the six genomes (shown above), some basic characters about the codon usage in synonymous codon repeat sequences are analyzed. The results show that some codons' usage in synonymous codon repeat sequences is different from the codon usage in all coding sequences; and the characteristic of codon repeat ability is given. We find that codon repeat ability is different, especially, for same base repeat codons, its repeat ability is low. There is distinct position bias for the same codon repeat segments in synonymous codon repeat sequences. Finally, we discuss the relationship of those characters with genome evolution.