一种基于卷积码模型的遗传序列分析方法

A method for analyzing genetic sequence based on a convolutional code model

【目的】研究通信纠错编码理论在生物学领域研究中的应用。【方法】基于纠错编码理论,将卷积码模型分析方法用于遗传序列的分析,结合密码子简并性以及碱基关联短程为主的特性,对卷积码模型的生成矩阵、编码长度和约束长度等参数进行讨论。对2种原核生物(Escherichia colistr.K-12 substr.MG1655和Staphylococcus epidermidisATCC 12228)与2种真核生物(Arabidopsis thaliana chromosome 4和Oryza sativa(japonica cultivar-group)chromosome 10)DNA序列翻译起始及终止的特征进行分析,并通过对不同卷积码模型的比较,确定合适的分析模型。【结果】在适当的分析模型下,分析结果在开放阅读框(ORF)起始端和终止端附近,显示出与起始密码子和终止密码子位置紧密关联的明显码距变化,而不适当的分析模型则使分析结果与生物意义的对应关系下降;分析方法对2种原核生物和2种真核生物具有较好的统一性。【结论】通信纠错编码模型与蕴含纠错机制的生物序列编码特性可以较好地结合,这对将纠错编码理论与生物学研究相结合具有一定的指导意义。

[Objective] The objective of this research was to study the application of error-correction coding theory of communication engineering in biological field. [Method] The principle of eonvolutional code was employed to analyze genetic sequence based on error-correction coding theory. The parameters, such as generator matrix, code length and constraint length, of the convolutional code models were designed and compared based on the degeneracy of codons and short-range dominance of bases correlation. The coding features of the translation initiation and termination of the DNA sequences of two prokaryotes （Escherichia coli str. K-12 substr. MG1655 and Staphylococcus epiderrnidis ATCC 12228） and two eukaryotes （Arabidopsis thaliana chromosome 4 and Oryza sativa （japonica cultivar-group） chromosome 10） were studied to search appropriate analysis model. [Result] Obvious changes of average code distance were observed near the initiation site and the termination site of the open reading frame （ORF） in appropriate models, and the parallelism between analysis results and biology sense descended in inappropriate models. The proposed method presents universality for the two prokaryotes and the two eukaryotes. [Conclusion] The analysis suggests that the error-correction coding model of communication engineering can be used to ana-lyze genetic sequences which contain error-correction mechanism,and it provides instructions to use errorcorrection coding theory for further study in biological field.