注释
基因组
基因组学
基因注释
基因组计划
顺序装配
计算生物学
资源(消歧)
数据科学
拟南芥
计算机科学
基因组浏览器
基因本体论
仿形(计算机编程)
生物
基因
转录组
生物信息学
遗传学
突变体
基因表达
操作系统
计算机网络
作者
Nidhin Sreekumar,Suvanish Kumar Valsala Sudarsanan
出处
期刊:Current Bioinformatics
[Bentham Science]
日期:2023-07-25
卷期号:18
标识
DOI:10.2174/1574893618666230725123211
摘要
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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