An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges.
An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges.
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DOI：
10.1093/bib/4.2.105
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发表时间：
2003-06-01
影响因子：
9.5
通讯作者：
Slezak, Tom
中科院分区：
文献类型：
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作者：
Chain, Patrick;Kurtz, Stefan;Slezak, Tom
劳伦斯利弗莫尔国家实验室（LLNL）的一个研究小组获得了一项任务，即利用计算工具加快用于病原体检测的DNA诊断技术的发展。这一工作将在本期的另一篇论文中描述（见第133-149页）。为了实现这一目标，有必要了解各种可用的比较基因组学工具的优点和局限性。综述了近年来用于多序列/基因组比对和子串比较的一些工具，并在适用于大规模应用的一般框架内进行了介绍。我们注意到，基因组比对在很多事情上都很重要，其中只有一项是病原体检测。了解基因功能、基因调控、基因网络、系统发育研究和其他方面的进化都依赖于准确的核酸和蛋白质序列比对。选择合适的工具可以在获得的结果质量和所需的努力方面产生很大的不同。
A team at the Lawrence Livermore National Laboratory (LLNL) was given the task of using computational tools to speed up the development of DNA diagnostics for pathogen detection. This work will be described in another paper in this issue (see pages 133-149). To achieve this goal it was necessary to understand the merits and limitations of the various available comparative genomics tools. A review of some recent tools for multisequence/genome alignment and substring comparison is presented, within the general framework of applicability to a large-scale application. We note that genome alignments are important for many things, only one of which is pathogen detection. Understanding gene function, gene regulation, gene networks, phylogenetic studies and other aspects of evolution all depend on accurate nucleic acid and protein sequence alignment. Selecting appropriate tools can make a large difference in the quality of results obtained and the effort required.