Dataset Information

A benchmark of transposon insertion detection tools using real data.

ABSTRACT: Background:Transposable elements (TEs) are an important source of genomic variability in eukaryotic genomes. Their activity impacts genome architecture and gene expression and can lead to drastic phenotypic changes. Therefore, identifying TE polymorphisms is key to better understand the link between genotype and phenotype. However, most genotype-to-phenotype analyses have concentrated on single nucleotide polymorphisms as they are easier to reliable detect using short-read data. Many bioinformatic tools have been developed to identify transposon insertions from resequencing data using short reads. Nevertheless, the performance of most of these tools has been tested using simulated insertions, which do not accurately reproduce the complexity of natural insertions. Results:We have overcome this limitation by building a dataset of insertions from the comparison of two high-quality rice genomes, followed by extensive manual curation. This dataset contains validated insertions of two very different types of TEs, LTR-retrotransposons and MITEs. Using this dataset, we have benchmarked the sensitivity and precision of 12 commonly used tools, and our results suggest that in general their sensitivity was previously overestimated when using simulated data. Our results also show that, increasing coverage leads to a better sensitivity but with a cost in precision. Moreover, we found important differences in tool performance, with some tools performing better on a specific type of TEs. We have also used two sets of experimentally validated insertions in Drosophila and humans and show that this trend is maintained in genomes of different size and complexity. Conclusions:We discuss the possible choice of tools depending on the goals of the study and show that the appropriate combination of tools could be an option for most approaches, increasing the sensitivity while maintaining a good precision.

SUBMITTER: Vendrell-Mir P

PROVIDER: S-EPMC6937713 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A benchmark of transposon insertion detection tools using real data.

Vendrell-Mir Pol P Barteri Fabio F Merenciano Miriam M González Josefa J Casacuberta Josep M JM Castanera Raúl R

Mobile DNA 20191230

<h4>Background</h4>Transposable elements (TEs) are an important source of genomic variability in eukaryotic genomes. Their activity impacts genome architecture and gene expression and can lead to drastic phenotypic changes. Therefore, identifying TE polymorphisms is key to better understand the link between genotype and phenotype. However, most genotype-to-phenotype analyses have concentrated on single nucleotide polymorphisms as they are easier to reliable detect using short-read data. Many bio ...[more]

PMID: 31892957

Similar Datasets

Project description:Botnets are some of the most recurrent cyber-threats, which take advantage of the wide heterogeneity of endpoint devices at the Edge of the emerging communication environments for enabling the malicious enforcement of fraud and other adversarial tactics, including malware, data leaks or denial of service. There have been significant research advances in the development of accurate botnet detection methods underpinned on supervised analysis but assessing the accuracy and performance of such detection methods requires a clear evaluation model in the pursuit of enforcing proper defensive strategies. In order to contribute to the mitigation of botnets, this paper introduces a novel evaluation scheme grounded on supervised machine learning algorithms that enable the detection and discrimination of different botnets families on real operational environments. The proposal relies on observing, understanding and inferring the behavior of each botnet family based on network indicators measured at flow-level. The assumed evaluation methodology contemplates six phases that allow building a detection model against botnet-related malware distributed through the network, for which five supervised classifiers were instantiated were instantiated for further comparisons-Decision Tree, Random Forest, Naive Bayes Gaussian, Support Vector Machine and K-Neighbors. The experimental validation was performed on two public datasets of real botnet traffic-CIC-AWS-2018 and ISOT HTTP Botnet. Bearing the heterogeneity of the datasets, optimizing the analysis with the Grid Search algorithm led to improve the classification results of the instantiated algorithms. An exhaustive evaluation was carried out demonstrating the adequateness of our proposal which prompted that Random Forest and Decision Tree models are the most suitable for detecting different botnet specimens among the chosen algorithms. They exhibited higher precision rates whilst analyzing a large number of samples with less processing time. The variety of testing scenarios were deeply assessed and reported to set baseline results for future benchmark analysis targeted on flow-based behavioral patterns.

Dataset Information

A benchmark of transposon insertion detection tools using real data.

Publications

A benchmark of transposon insertion detection tools using real data.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets