Whole-Genome Alignment: Methods, Challenges, and Future Directions

被引：5

作者：

Saada, Bacem ^{[1
]}

Zhang, Tianchi ^{[2
]}

Siga, Estevao ^{[3
]}

Zhang, Jing ^{[3
,4
]}

Magalhaes Muniz, Maria Malane ^{[1
]}

机构：

[1] Univ Guelph, Anim Biosci Dept, Guelph, ON N1G 2W1, Canada

[2] Chongqing Jiaotong Univ, Sch Informat Sci & Engn, Chongqing 400074, Peoples R China

[3] Univ Jinan, Sch Informat Sci & Engn, Jinan 250022, Peoples R China

[4] Shandong Prov Key Lab Network Based Intelligent Co, Jinan 250022, Peoples R China

来源：

APPLIED SCIENCES-BASEL | 2024年 / 14卷 / 11期

基金：

中国国家自然科学基金;

关键词：

anchors; graphs; high-throughput sequencing; suffix trees; hashing; whole-genome alignment; MULTIPLE SEQUENCE ALIGNMENT; SCALE; DIALIGN; PRIMER; TOOLS; RNA;

D O I：

10.3390/app14114837

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

Whole-genome alignment (WGA) is a critical process in comparative genomics, facilitating the detection of genetic variants and aiding our understanding of evolution. This paper offers a detailed overview and categorization of WGA techniques, encompassing suffix tree-based, hash-based, anchor-based, and graph-based methods. It elaborates on the algorithmic properties of these tools, focusing on performance and methodological aspects. This paper underscores the latest progress in WGA, emphasizing the increasing capacity to manage the growing intricacy and volume of genomic data. However, the field still grapples with computational and biological hurdles affecting the precision and speed of WGA. We explore these challenges and potential future solutions. This paper aims to provide a comprehensive resource for researchers, deepening our understanding of WGA tools and their applications, constraints, and prospects.

引用

页数：29

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