arXiv 2201.051982022-01-13q-bio.GNcs.DS

多基因组分析框架：所有 SARS-CoV-2 完整变异株案例

Multiple Genome Analytics Framework: The Case of All SARS-CoV-2 Complete Variants

Konstantinos Xylogiannopoulos

DOI：: 10.1016/j.jbiotec.2022.09.015

AI总结：

本文提出 Multiple Genome Analytics Framework，利用 O(nlogn) 的文本挖掘与模式检测算法，从 30 余万条 SARS-CoV-2 基因组中一次性发现长度至 60 nt 的重复模式，支撑比对、回文、串联重复及 PCR 引物等分析。

摘要：

模式检测与字符串匹配是计算机科学中的基础问题，而生物信息学和计算生物学的加速发展已使其成为这两个学科的核心主题。SARS-CoV-2 疫情使此类问题更具挑战性：由于持续突变，每周都会发现数百或数千个新的基因组变异株，因此迫切需要快速而准确的分析。对序列比对等基因组分析计算工具的需求非常重要，尽管在多数情况下所需资源和计算能力极其庞大。本文提出的 Multiple Genome Analytics Framework（多基因组分析框架）结合了专为文本挖掘和模式检测构建的数据结构与算法，能够以最少资源同时高效处理若干计算生物学和生物信息学问题。只需执行一次高级算法，其空间和时间复杂度均为 O(nlogn)，即可获得多条基因组序列中存在的所有重复模式的知识，并且这些信息可由其他元算法用于进一步的元分析。通过分析超过 300,000 条 SARS-CoV-2 基因组序列，并检测这些序列中长度至多 60 个核苷酸的所有重复模式，展示了所提框架的潜力。这些结果已被用于回答诸多问题，例如所有变异株之间的共同模式、序列比对、回文和串联重复检测、不同生物体基因组比较、聚合酶链式反应引物检测等。

英文摘要：

Pattern detection and string matching are fundamental problems in computer science and the accelerated expansion of bioinformatics and computational biology have made them a core topic for both disciplines. The SARS-CoV-2 pandemic has made such problems more demanding with hundreds or thousands of new genome variants discovered every week, because of constant mutations, and there is a desperate need for fast and accurate analyses. The requirement for computational tools for genomic analyses, such as sequence alignment, is very important, although, in most cases the resources and computational power required are enormous. The presented Multiple Genome Analytics Framework combines data structures and algorithms, specifically built for text mining and pattern detection, that can help to efficiently address several computational biology and bioinformatics problems concurrently with minimal resources. A single execution of advanced algorithms, with space and time complexity O(nlogn), is enough to acquire knowledge on all repeated patterns that exist in multiple genome sequences and this information can be used from other meta-algorithms for further meta-analyses. The potential of the proposed framework is demonstrated with the analysis of more than 300,000 SARS-CoV-2 genome sequences and the detection of all repeated patterns with length up to 60 nucleotides in these sequences. These results have been used to provide answers to questions such as common patterns among all variants, sequence alignment, palindromes and tandem repeats detection, different organism genome comparisons, polymerase chain reaction primers detection, etc.

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