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字符串"ACGT"数组的基因组组合组成:对数据结构准确性和性能挑战的审查

Sherif Magdy Mohamed Abdelaziz Barakat¹, Roselina Sallehuddin¹, Siti Sophiayati Yuhaniz²

¹Computer Science, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia.

PeerJ. Computer science

|August 7, 2023

概括

基因组组装面临重复序列和大数据集的挑战. 本次审查建议结合重复识别方法和优化混合方法,以提高准确性和性能.

科学领域:

基因组学和生物信息学
计算生物学计算生物学
基因组组装的基因组组装

背景情况:

测序技术的进步产生了大量的基因组数据,这给准确的基因组组装带来了挑战.
基因组中的重复序列 (重复) 引入了模两可,导致了错误组装,并在 de novo 和参考引导组装方法中降低了准确性.
大量的读取数据集给基因组组装算法带来了重大性能挑战.

研究的目的:

提供对基因组组装研究的广泛审查,重点关注准确性和性能优化.
为了突出最近的发展和在基因组组装过程中处理重复序列的局限性.
通过整合有关基因组组装方法的信息来支持研究人员.

主要方法:

对基因组组装现有文献的审查,包括 de novo,参考指导和混合方法.
分析重复识别方法及其对组装准确性的影响.
评估性能优化策略,如数据结构索引和并行化.

主要成果:

当前的重复识别方法在检测不同长度和类型的重复中存在局限性,这会影响组件的准确性.
混合组装方法显示出希望,但面临的挑战是重复序列,增加的计算成本和时间强度.
基因组组装中的并行化,特别是重叠和读取对齐,在混合策略中并未完全实施.

结论:

建议结合多种重复识别方法,以提高混合组装前重复检测的准确性.
建议将基因组索引与并行化整合起来,以优化混合组装方法的性能.
需要进一步的研究来充分实施和优化混合基因组组装框架内的并行化.

关键词:

基因组分析基因组分析基因组组装组的基因组组装组基因组组合错误的发生索引基因组数据的数据.平行化基因组数据.重复的基因组序列识别识别方法

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