Bioinformatic Resources for Plant Genomic Research

IF 2.4 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Current Bioinformatics Pub Date : 2023-07-25 DOI:10.2174/1574893618666230725123211

N. Sreekumar, Suvanish Kumar Valsala Sudarsanan

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引用次数: 0

Abstract

Genome assembly and annotation are crucial steps in plant genomics research as they provide valuable insights into plant genetic makeup, gene regulation, evolutionary history, and biological processes. In the emergence of high-throughput sequencing technologies, a plethora of genome assembly tools have been developed to meet the diverse needs of plant genome researchers. Choosing the most suitable tool to suit a specific research need can be daunting due to the complex and varied nature of plant genomes and reads from the sequencers. To assist informed decision-making in selecting the appropriate genome assembly and annotation tool(s), this review offers an extensive overview of the most widely used genome and transcriptome assembly tools. The review covers the specific information on each tool in tabular data, and the data types it can process. In addition, the review delves into transcriptome assembly tools, plant resource databases, and repositories (12 for Arabidopsis, 9 for Rice, 5 for Tomato, and 8 general use resources), which are vital for gene expression profiling and functional annotation and ontology tools that facilitate data integration and analysis.

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植物基因组研究的生物信息学资源

基因组组装和注释是植物基因组学研究的关键步骤，因为它们为植物基因构成、基因调控、进化史和生物过程提供了有价值的见解。随着高通量测序技术的出现，已经开发了大量的基因组组装工具来满足植物基因组研究人员的各种需求。由于植物基因组和测序仪读数的复杂性和多样性，选择最适合特定研究需求的工具可能会令人望而却步。为了帮助知情决策选择合适的基因组组装和注释工具，本综述对最广泛使用的基因组和转录组组装工具进行了广泛概述。审查涵盖了表格数据中每个工具的具体信息，以及它可以处理的数据类型。此外，该综述深入研究了转录组组装工具、植物资源数据库和存储库（12个用于拟南芥，9个用于水稻，5个用于番茄，8个用于通用资源），这些对于促进数据集成和分析的基因表达谱、功能注释和本体论工具至关重要。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Current Bioinformatics 生物-生化研究方法

CiteScore

6.60

自引率

2.50%

发文量

审稿时长

>12 weeks

期刊介绍： Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth/mini-reviews, research papers and guest edited thematic issues written by leaders in the field, covering a wide range of the integration of biology with computer and information science. The journal focuses on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.