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首页> 外文期刊>Nucleic Acids Research >Issues in bioinformatics benchmarking: the case study of multiple sequence alignment
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Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

机译：生物信息学基准测试中的问题：多序列比对的案例研究

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摘要

The post-genomic era presents many new challenges for the field of bioinformatics. Novel computational approaches are now being developed to handle the large, complex and noisy datasets produced by high throughput technologies. Objective evaluation of these methods is essential (i) to assure high quality, (ii) to identify strong and weak points of the algorithms, (iii) to measure the improvements introduced by new methods and (iv) to enable non-specialists to choose an appropriate tool. Here, we discuss the development of formal benchmarks, designed to represent the current problems encountered in the bioinformatics field. We consider several criteria for building good benchmarks and the advantages to be gained when they are used intelligently. To illustrate these principles, we present a more detailed discussion of benchmarks for multiple alignments of protein sequences. As in many other domains, significant progress has been achieved in the multiple alignment field and the datasets have become progressively more challenging as the existing algorithms have evolved. Finally, we propose directions for future developments that will ensure that the bioinformatics benchmarks correspond to the challenges posed by the high throughput data.
机译：后基因组时代对生物信息学领域提出了许多新的挑战。现在正在开发新颖的计算方法来处理由高通量技术产生的大型，复杂和嘈杂的数据集。这些方法的客观评估对于（i）确保高质量，（ii）识别算法的优缺点，（iii）衡量新方法引入的改进以及（iv）使非专业人员能够选择这些方法至关重要。适当的工具。在这里，我们讨论正式基准的开发，这些基准旨在代表生物信息学领域当前遇到的问题。我们考虑了建立良好基准的几个标准，以及在智能地使用它们时可以获得的优势。为了说明这些原理，我们提出了蛋白质序列多重比对的基准的更详细的讨论。与许多其他领域一样，在多重比对领域已取得了重大进展，并且随着现有算法的发展，数据集变得越来越具有挑战性。最后，我们提出了未来发展的方向，这些方向将确保生物信息学基准测试与高通量数据带来的挑战相对应。

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