A hitchhiker's guide to expressed sequence tag (EST) analysis
A hitchhiker's guide to expressed sequence tag (EST) analysis
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DOI：
10.1093/bib/bbl015
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发表时间：
2007-01-01
影响因子：
9.5
通讯作者：
Ranganathan, Shoba
中科院分区：
文献类型：
--
作者：
Nagaraj, Shivashankar H.;Gasser, Robin B.;Ranganathan, Shoba
表达序列标签（EST）测序项目正在进行中的许多生物体，产生数百万短，单程核苷酸序列读取，积累在EST数据库。广泛的计算策略已经开发出组织和分析小规模和大规模的EST数据的基因发现，转录和单核苷酸多态性分析以及功能注释的推定基因产物。本文综述了EST在基因组时代的重要性、EST的性质及其应用。比较了不同研究小组在EST分析的每一步所采用的方法。还确定了组织和分析不断增加的EST数据方面面临的挑战。已汇编了用于EST预处理、聚类和汇编、数据库匹配和功能注释的最适当的软件工具（可在线查阅http：//biolinfo.org/EST）。我们提出了一个EST分析的路线图，以加快EST数据集的有效分析。对EST分析平台的调查显示，它们都在下游功能注释之前终止，包括基因本体，模体/模式分析和通路定位。
Expressed sequence tag (EST) sequencing projects are underway for numerous organisms, generating millions of short, single-pass nucleotide sequence reads, accumulating in EST databases. Extensive computational strategies have been developed to organize and analyse both small- and large-scale EST data for gene discovery, transcript and single nucleotide polymorphism analysis as well as functional annotation of putative gene products. We provide an overview of the significance of ESTs in the genomic era, their properties and the applications of ESTs. Methods adopted for each step of EST analysis by various research groups have been compared. Challenges that lie ahead in organizing and analysing the ever increasing EST data have also been identified. The most appropriate software tools for EST pre-processing, clustering and assembly, database matching and functional annotation have been compiled (available online from http://biolinfo.org/EST). We propose a road map for EST analysis to accelerate the effective analyses of EST data sets. An investigation of EST analysis platforms reveals that they all terminate prior to downstream functional annotation including gene ontologies, motif/pattern analysis and pathway mapping.