Method for the design of mRNA detecting genechip based on codon usage bias

To decrease the number of possibl probles during the process of chip design, the codon use frequency table of the to-be-detect mRNA sequence was first forecasted, and the coding codons for each amino acid were predicted. By this method, the number of probes was reduced to 4.47%. At the same time, such codon usage principles as C-G separation and G-T base-pairing were also considered. As a result, the number of probes was decreased to 4.25%. The optimum codon usage table was used to dramatically decrease the number of probes to 0.20% when the specificity of probes was not strictly demanded. As a result, the detecting information per square unit on genechip can be increased significantly.