ArticleGenome research2006
Identification of transposable elements using multiple alignments of related genomes.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 53 citations in OpenAlex.
- Comparative genomics reveals LINE-1 recombination with diverse RNAs.Cell genomics · 2026Article
- Methodologies for theGenes · 2022Review
- Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster.Nucleic acids research · 2020Article
- Typing methods based on whole genome sequencing data.One health outlook · 2020Review
- Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila.Genome biology and evolution · 2018Article
- A machine learning based framework to identify and classify long terminal repeat retrotransposons.PLoS computational biology · 2018Article
- Article
- Solving the master equation for Indels.BMC bioinformatics · 2017Article
- A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching.Evolutionary bioinformatics online · 2016Article
- Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.BMC bioinformatics · 2015Article
- A call for benchmarking transposable element annotation methods.Mobile DNA · 2015Article
- Mobilomics in Saccharomyces cerevisiae strains.BMC bioinformatics · 2013Article
- An automated homology-based approach for identifying transposable elements.BMC bioinformatics · 2011Article
- Cgaln: fast and space-efficient whole-genome alignment.BMC bioinformatics · 2010Article
- Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila.Genome research · 2010Article
- Contrasting patterns of transposable element insertions in Drosophila heat-shock promoters.PloS one · 2009Article
- The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes.Plant methods · 2009Article
- Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data.PloS one · 2009Article
- LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice.BMC genomics · 2008Article
- Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice.Plant physiology · 2008Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate genome-wide cataloging of transposable elements (TEs) will facilitate our understanding of mobile DNA evolution, expose the genomic effects of TEs on the host genome, and improve the quality of assembled genomes. Using the availability of several nearly complete Drosophila genomes and developments in whole genome alignment methods, we introduce a large-scale comparative method for identifying repetitive mobile DNA regions. These regions are highly enriched for transposable elements. Our method has two main features distinguishing it from other repeat-finding methods. First, rather than relying on sequence similarity to determine the location of repeats, the genomic artifacts of the transposition mechanism itself are systematically tracked in the context of multiple alignments. Second, we can derive bounds on the age of each repeat instance based on the phylogenetic species tree. We report results obtained using both complete and draft sequences of four closely related Drosophila genomes and validate our results with manually curated TE annotations in the Drosophila melanogaster euchromatin. We show the utility of our findings in exploring both transposable elements and their host genomes: In the study of TEs, we offer predictions for novel families, annotate new insertions of known families, and show data that support the hypothesis that all known TE families in D. melanogaster were recently active; in the study of the host, we show how our findings can be used to determine shifts in the eu-heterochromatin junction in the pericentric chromosome regions.
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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.