ArticleBioinformatics (Oxford, England)2011
MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed.
- Communication Lower-Bounds for Distributed-Memory Computations for Mass Spectrometry based Omics Data.Journal of parallel and distributed computing · 2022Article
- Parameter discovery in stochastic biological models using simulated annealing and statistical model checking.International journal of bioinformatics research and applications · 2014Article
- MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information.BMC bioinformatics · 2013Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryA MapReduce-based implementation called MR-MSPolygraph for parallelizing peptide identification from mass spectrometry data is presented. The underlying serial method, MSPolygraph, uses a novel hybrid approach to match an experimental spectrum against a combination of a protein sequence database and a spectral library. Our MapReduce implementation can run on any Hadoop cluster environment. Experimental results demonstrate that, relative to the serial version, MR-MSPolygraph reduces the time to solution from weeks to hours, for processing tens of thousands of experimental spectra. Speedup and other related performance studies are also reported on a 400-core Hadoop cluster using spectral datasets from environmental microbial communities as inputs. AVAILABILITY: The source code along with user documentation are available on http://compbio.eecs.wsu.edu/MR-MSPolygraph. CONTACT: ananth@eecs.wsu.edu; william.cannon@pnnl.gov. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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