ArticleGenome biology2006
Identifying repeat domains in large genomes.
Article in Genome biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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Who cites it
22 citing papers in PubMed.
- Chromosome-scale reference genome assembly and annotation of Prunus scopulorum.Scientific data · 2026Article
- DREAM-Stellar: parallel and space efficient exact local alignment.BMC bioinformatics · 2026Article
- NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model.BMC bioinformatics · 2025Article
- Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control.Plant communications · 2024Article
- Article
- Dissecting the genetic basis of heterosis in elite super-hybrid rice.Plant physiology · 2023Article
- Chromosome-level genome assembly provides new insights into Japanese chestnut (Frontiers in plant science · 2022Article
- The piRNA pathway is essential for generating functional oocytes in golden hamsters.Nature cell biology · 2021Article
- Whole-genome de novo assemblies reveal extensive structural variations and dynamic organelle-to-nucleus DNA transfers in African and Asian rice.The Plant journal : for cell and molecular biology · 2020Article
- Comparative analysis of miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species.BMC plant biology · 2019Article
- Genomic and transcriptomic analyses of the tangerine pathotype of Alternaria alternata in response to oxidative stress.Scientific reports · 2016Article
- Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats.Bioinformatics (Oxford, England) · 2016Article
- Recurrent evolution of melanism in South American felids.PLoS genetics · 2015Article
- Review of general algorithmic features for genome assemblers for next generation sequencers.Genomics, proteomics & bioinformatics · 2012Review
- Assembly algorithms for next-generation sequencing data.Genomics · 2010Review
- UCbase & miRfunc: a database of ultraconserved sequences and microRNA function.Nucleic acids research · 2009Article
- Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data.Source code for biology and medicine · 2008Article
- Empirical comparison of ab initio repeat finding programs.Nucleic acids research · 2008Article
- Short read fragment assembly of bacterial genomes.Genome research · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a graph-based method for the analysis of repeat families in a repeat library. We build a repeat domain graph that decomposes a repeat library into repeat domains, short subsequences shared by multiple repeat families, and reveals the mosaic structure of repeat families. Our method recovers documented mosaic repeat structures and suggests additional putative ones. Our method is useful for elucidating the evolutionary history of repeats and annotating de novo generated repeat libraries.
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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.