ArticleGene2007
Improved repeat identification and masking in Dipterans.
Article in Gene, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
54 citing papers in PubMed, 92 citations in OpenAlex.
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- Characterization of transposable elements within the Bemisia tabaci species complex.Mobile DNA · 2022Article
- The bowfin genome illuminates the developmental evolution of ray-finned fishes.Nature genetics · 2021Article
- Draft Genome Sequence of Oleaginous YeastMicrobiology resource announcements · 2020Article
- The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae).Genome biology and evolution · 2019Article
- Updated Genome Assembly and Annotation forG3 (Bethesda, Md.) · 2019Article
- Draft Genome Sequences of Basidiomycetous Epiphytic Phylloplane Yeast Type StrainsMicrobiology resource announcements · 2019Article
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- GAAP: A Genome Assembly + Annotation Pipeline.BioMed research international · 2019Article
- Computational tools to unmask transposable elements.Nature reviews. Genetics · 2018Review
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- Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination.PLoS biology · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 5 institutions in 1 country.
Funding
Abstract
Repetitive sequences are a major constituent of many eukaryote genomes and play roles in gene regulation, chromosome inheritance, nuclear architecture, and genome stability. The identification of repetitive elements has traditionally relied on in-depth, manual curation and computational determination of close relatives based on DNA identity. However, the rapid divergence of repetitive sequence has made identification of repeats by DNA identity difficult even in closely related species. Hence, the presence of unidentified repeats in genome sequences affects the quality of gene annotations and annotation-dependent analyses (e.g. microarray analyses). We have developed an enhanced repeat identification pipeline using two approaches. First, the de novo repeat finding program PILER-DF was used to identify interspersed repetitive elements in several recently finished Dipteran genomes. Repeats were classified, when possible, according to their similarity to known elements described in Repbase and GenBank, and also screened against annotated genes as one means of eliminating false positives. Second, we used a new program called RepeatRunner, which integrates results from both RepeatMasker nucleotide searches and protein searches using BLASTX. Using RepeatRunner with PILER-DF predictions, we masked repeats in thirteen Dipteran genomes and conclude that combining PILER-DF and RepeatRunner greatly enhances repeat identification in both well-characterized and un-annotated genomes.
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What OpenQuestion holds
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.