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Reproducible and replicable comparisons using SummarizedBenchmark.

ABSTRACT: Summary:Benchmark studies are widely used to compare and evaluate tools developed for answering various biological questions. Despite the popularity of these comparisons, the implementation is often ad hoc, with little consistency across studies. To address this problem, we developed SummarizedBenchmark, an R package and framework for organizing and structuring benchmark comparisons. SummarizedBenchmark defines a general grammar for benchmarking and allows for easier setup and execution of benchmark comparisons, while improving the reproducibility and replicability of such comparisons. We demonstrate the wide applicability of our framework using four examples from different applications. Availability and implementation:SummarizedBenchmark is an R package available through Bioconductor (http://bioconductor.org/packages/SummarizedBenchmark). Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Kimes PK

PROVIDER: S-EPMC6298041 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Reproducible and replicable comparisons using SummarizedBenchmark.

Kimes Patrick K PK Reyes Alejandro A

Bioinformatics (Oxford, England) 20190101 1

<h4>Summary</h4>Benchmark studies are widely used to compare and evaluate tools developed for answering various biological questions. Despite the popularity of these comparisons, the implementation is often ad hoc, with little consistency across studies. To address this problem, we developed SummarizedBenchmark, an R package and framework for organizing and structuring benchmark comparisons. SummarizedBenchmark defines a general grammar for benchmarking and allows for easier setup and execution ...[more]

PMID: 30016409

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Project description:Chemotaxis is the process by which motile bacteria sense their chemical environment and move towards more favourable conditions. Escherichia coli utilises a single sensory pathway, but little is known about signalling pathways in species with more complex systems.To investigate whether chemotaxis pathways in other bacteria follow the E. coli paradigm, we analysed 206 species encoding at least 1 homologue of each of the 5 core chemotaxis proteins (CheA, CheB, CheR, CheW and CheY). 61 species encode more than one of all of these 5 proteins, suggesting they have multiple chemotaxis pathways. Operon information is not available for most bacteria, so we developed a novel statistical approach to cluster che genes into putative operons. Using operon-based models, we reconstructed putative chemotaxis pathways for all 206 species. We show that cheA-cheW and cheR-cheB have strong preferences to occur in the same operon as two-gene blocks, which may reflect a functional requirement for co-transcription. However, other che genes, most notably cheY, are more dispersed on the genome. Comparison of our operons with shuffled equivalents demonstrates that specific patterns of genomic location may be a determining factor for the observed in vivo chemotaxis pathways. We then examined the chemotaxis pathways of Rhodobacter sphaeroides. Here, the PpfA protein is known to be critical for correct partitioning of proteins in the cytoplasmically-localised pathway. We found ppfA in che operons of many species, suggesting that partitioning of cytoplasmic Che protein clusters is common. We also examined the apparently non-typical chemotaxis components, CheA3, CheA4 and CheY6. We found that though variants of CheA proteins are rare, the CheY6 variant may be a common type of CheY, with a significantly disordered C-terminal region which may be functionally significant.We find that many bacterial species potentially have multiple chemotaxis pathways, with grouping of che genes into operons likely to be a major factor in keeping signalling pathways distinct. Gene order is highly conserved with cheA-cheW and cheR-cheB blocks, perhaps reflecting functional linkage. CheY behaves differently to other Che proteins, both in its genomic location and its putative protein interactions, which should be considered when modelling chemotaxis pathways.

Dataset Information

Reproducible and replicable comparisons using SummarizedBenchmark.

Publications

Reproducible and replicable comparisons using SummarizedBenchmark.

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