Construction Of Multifunctional Codon Analysis And Optimization Platform And Its Application Study

In the process of genetic information passing through generations,coding and decoding of the genetic information is very important.Codon refers to the three adjacent bases on the mRNA chain that determine an amino acid,also called triplet codons.Codon has many characteristics,which has been a hot topic in theoretic and synthetic biology researches.The researchers found that 20 common amino acids correspond to 61 different codons.Except for methionine and tryptophan,each amino acid corresponds to multiple codons,which makes the degeneracy of codon.However,it is found that in different species,the use of synonymous codons is not a random event.Some species prefer to use certain kinds of codons,which termed as the Codon Usage Bias(CUB).In the field of phylogeny and evolutionary research,codon usage is often used as an indicator.In addition,in the field of synthetic biology,researchers use CUB to optimize genes.They use the codon preferred by host cells to replace the codon of alien genes,so as to improve the expression of alien genes in the host.In addition,some scientists use rare codon replacement to make attenuated vaccine.Due to its wide application,researchers have put forward many quantitative indexes of codon analysis,such as Relative Synonymous Codon Usage(RSCU),Effective Codon Number(ENC),Codon Adaptation Index(CAI),ENC-GC3 s plot analysis,PR2 plot analysis,Codon Pair Bias(CPB),etc.,but many indexes are not easy to use.Some indexes need the users to write programs by themselves,which causes certain difficulties for many wet-lab researchers and hinders the progress of their research.For the reasons above,this study finds out the indicators and contents of codon analysis commonly used and newly proposed by researchers in the current scientific research field through literature collection.We use Python script to achieve all the analysis,and builds a multifunctional analysis and optimization platform based on Django.The platform is easy to use,fully-featured,and under active development,providing convenience for codon analysis.In addition,this study also developed a codon pair optimization algorithm,which was integrated into the optimization module of the platform,providing a new thought for the optimization.At the end of this paper,two cases are used to show the advantages of using this codon analysis and optimization platform.The first case shows that using the codon analysis function can quickly complete the analysis of the whole genome codon usage bias of three plants,and gives the comparative results.The second case shows that heterologous gene expression can be improved by optimizing codon on this platform.It is found that the optimization algorithm based on codon pair bias has potential advantages over the traditional optimization algorithm which is based on single codon bias.