ArticlePLoS computational biology2005
ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun.
Article in PLoS computational biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 107 citations in OpenAlex.
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- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes.Nature communications · 2021Article
- A sensitive repeat identification framework based on short and long reads.Nucleic acids research · 2021Article
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- Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins.Scientific reports · 2020Article
- Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning.International journal of molecular sciences · 2019Review
- MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies.Mobile DNA · 2019Article
- Estimating theCurrent genomics · 2019Article
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- Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.Nature communications · 2017Article
- Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories.Mobile DNA · 2017Review
- Characterization of new transposable element sub-families from white clover (Trifolium repens) using PCR amplification.Genetica · 2016Article
- phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats.Bioinformatics (Oxford, England) · 2016Article
- piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis.PLoS genetics · 2015Article
- Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.BMC bioinformatics · 2015Article
- RiTE database: a resource database for genus-wide rice genomics and evolutionary biology.BMC genomics · 2015Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 3 countries.
Funding
Abstract
We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.
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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.