ArticleBioinformatics (Oxford, England)2016
phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Article
- Multi-omics analysis reveals criticaliScience · 2025Article
- Ongoing Rapid Evolution of a Post-Y Region Revealed by Chromosome-Scale Genome Assembly of a Hexaploid Monoecious Persimmon (Diospyros kaki).Molecular biology and evolution · 2023Article
- Software evaluation for de novo detection of transposons.Mobile DNA · 2022Article
- Methodologies for theGenes · 2022Review
- Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection.Plant physiology · 2019Article
- ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation.BMC genomics · 2019Article
- Computational tools to unmask transposable elements.Nature reviews. Genetics · 2018Review
- An improved approach for reconstructing consensus repeats from short sequence reads.BMC genomics · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationTransposable elements (TEs) and repetitive DNA make up a sizable fraction of Eukaryotic genomes, and their annotation is crucial to the study of the structure, organization, and evolution of any newly sequenced genome. Although RepeatMasker and nHMMER are useful for identifying these repeats, they require a pre-compiled repeat library-which is not always available. De novo identification tools such as Recon, RepeatScout or RepeatGluer serve to identify TEs purely from sequence content, but are either limited by runtimes that prohibit whole-genome use or degrade in quality in the presence of substitutions that disrupt the sequence patterns.
resultsphRAIDER is a de novo TE identification tool that address the issues of excessive runtime without sacrificing sensitivity as compared to competing tools. The underlying model is a new definition of elementary repeats that incorporates the PatternHunter spaced seed model, allowing for greater sensitivity in the presence of genomic substitutions. As compared with the premier tool in the literature, RepeatScout, phRAIDER shows an average 10× speedup on any single human chromosome and has the ability to process the whole human genome in just over three hours. Here we discuss the tool, the theoretical model underlying the tool, and the results demonstrating its effectiveness. AVAILABILITY AND IMPLEMENTATION: phRAIDER is an open source tool available from https://github.com/karroje/phRAIDER CONTACT: : karroje@miamiOH.edu or SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.