Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-12-05

AUTHORS

Steven Lewis, Attila Csordas, Sarah Killcoyne, Henning Hermjakob, Michael R Hoopmann, Robert L Moritz, Eric W Deutsch, John Boyle

ABSTRACT

BackgroundFor 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.ResultsWe 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.ConclusionThe 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. More... »

PAGES

324

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-13-324

DOI

http://dx.doi.org/10.1186/1471-2105-13-324

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1032496631

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/23216909


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