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

Jianmin Ma, Wanjun Gu, Tong Zhou, Xiao Sun, Zuhong Lu

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)581-585
Number of pages5
JournalDongnan Daxue Xuebao (Ziran Kexue Ban)/Journal of Southeast University (Natural Science Edition)
Issue number4
StatePublished - Jul 2002
Externally publishedYes


  • C-G selective separation
  • Codon usage bias
  • G-T base-pairing
  • Probe optimization
  • mRNA detecting genechip

ASJC Scopus subject areas

  • Engineering(all)


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