Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
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DOI：
10.1186/1471-2105-13-324
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发表时间：
2012-12-05
影响因子：
3
通讯作者：
Boyle J
中科院分区：
文献类型：
--
作者：
Lewis S;Csordas A;Killcoyne S;Hermjakob H;Hoopmann MR;Moritz RL;Deutsch EW;Boyle J
对于基于鸟枪式质谱学的蛋白质组学来说，最昂贵的计算步骤是将光谱与日益庞大的序列数据库及其翻译后修饰与已知质量进行匹配。每台质谱仪都能以惊人的速度产生数据，搜索的范围也在不断扩大。因此，需要解决方案来提高我们执行这些搜索的能力。我们提出了一个专门为在Hadoop MapReduce分布式计算框架上高效运行而设计的序列数据库搜索引擎。搜索引擎实现了K-Score算法，为与原始实现相同的输入文件生成类似的输出。展示了该系统的可扩展性，并讨论了开发这种分布式处理所需的体系结构。该软件在处理大型多肽数据库、大量修改和大量光谱方面是可扩展的。性能随群集中处理器数量的增加而扩展，允许吞吐量随可用资源的增加而扩展。
For shotgun mass spectrometry based proteomics the most computationally expensive step is in matching the spectra against an increasingly large database of sequences and their post-translational modifications with known masses. Each mass spectrometer can generate data at an astonishingly high rate, and the scope of what is searched for is continually increasing. Therefore solutions for improving our ability to perform these searches are needed. We present a sequence database search engine that is specifically designed to run efficiently on the Hadoop MapReduce distributed computing framework. The search engine implements the K-score algorithm, generating comparable output for the same input files as the original implementation. The scalability of the system is shown, and the architecture required for the development of such distributed processing is discussed. The software is scalable in its ability to handle a large peptide database, numerous modifications and large numbers of spectra. Performance scales with the number of processors in the cluster, allowing throughput to expand with the available resources.
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