De novo identification of repeat families in large genomes

By Alkes L Price, Neil Christopher Jones, Pavel A. Pevzner. Intelligent Systems in Molecular Biology, 2005

2,042 citations recorded by the source corpus.

Subfields: Cellular and Molecular Neuroscience, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e8dba5bf84c7c3cdae3648a76d0af6ff1e393009

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Citations in the corpus

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis (2013, methodology): “It has been hypothesized that AMF maintain an assemblage of genetically different nuclei (heterokaryosis) and transmit them from generation to generation (12, 13).”
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data (2011, positive): “Seed selection by Inchworm was largely inspired by similar methods implemented in the RepeatScout algorith”
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes (2012, methodology): “Genomic assembly scaffolds of each genomes were masked using RepeatScout (9) and RepeatMasker (10) and the RepBase (11) library of fungal repeats.”
RepSeq – A database of amino acid repeats present in lower eukaryotic pathogens (2007, positive): “While a large number of applications have been developed for detecting and analysing genome-level repeats (e.g. Repeat Masker [16], Repeat Scout [17] and Tandem Repeats Finder [18]), there are very few applications/databases which deal with proteome-level repeats.”
Repbase Update, a database of repetitive elements in eukaryotic genomes (2015, methodology): “There are a number of tools designed to automate TE identification and/or annotation, such as RECON [14], RepeatScout [15], PILER [16], RepeatModeler [17], Dfam [18], REPCLASS [19], REPET [20], and PASTEC [21], with none having distinct advantages [20, 22].”
Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions (2012, methodology): “REP elements were defined by searching for repeat sequences greater than 30 nt in length that occurred more than 10 times within individual genomes using RepeatScout [154].”
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline (2019, methodology): “Comparison of General Repeat Annotators We benchmarked five general repeat annotators, including RECON [43], RepeatScout [26], RepeatModeler [28], Red [27], and Generic Repeat Finder (GRF) (https://github.com/bioinfolabmu/GenericRepeatFinder), as well as a repeat database Repbase [30], which is wide”