In this study, we introduce a novel bioinformatics program, Spore-associated Symbiotic Microbes Position-specific Function (SeSaMe PS Function), for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi. The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure, namely amino acid usages, codon usages, and codon contexts of 3-codon DNA 9-mers. SeSaMe PS Function searches a query sequence against reference sequence database, identifies 3-codon DNA 9-mers with structural roles, and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera. The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset. 3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions. The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications. SeSaMe PS Function is freely accessible at www.fungalsesame.org.

在这项研究中，我们介绍了一种新的生物信息学程序，孢子相关共生微生物位置特异性功能( SeSaMe PS 功能)，用于对源自宏基因组的短序列进行位置特异性功能分析丛枝菌根真菌的测序数据。该程序的独特优势在于基于源自蛋白质二级结构的属特异性序列特性创建的数据库，即氨基酸使用、密码子使用和 3-密码子 DNA 9-mers 的密码子上下文。SeSaMe PS Function 根据参考序列数据库搜索查询序列，识别具有结构作用的 3 密码子 DNA 9 聚体，并创建包含来自 54 个细菌和真菌属的 3 密码子 DNA 9 聚体的密码子使用偏差的比较数据集。该程序将相关主成分分析结合 K-means 聚类方法应用于比较数据集。3-密码子 DNA 9-mers 作为唯一成员或只有少数成员聚集在一起，通常是结构和功能独特的位点，可为重要的分子相互作用提供有用的见解。该程序提供了一种从宏基因组测序中研究短序列功能的通用方法，并具有广泛的应用。SeSaMe PS 功能可在 www.fungalsesame.org 上免费访问。