ArticleBMC genomics2008
Automated paleontology of repetitive DNA with REANNOTATE.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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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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Who cites it
21 citing papers in PubMed, 38 citations in OpenAlex.
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- Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning.International journal of molecular sciences · 2019Review
- Long-read sequencing data analysis for yeasts.Nature protocols · 2018Article
- Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome.Genome research · 2018Article
- Deficiency of microRNAScience (New York, N.Y.) · 2017Article
- EnHERV: Enrichment analysis of specific human endogenous retrovirus patterns and their neighboring genes.PloS one · 2017Article
- LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on Genomes.Frontiers in plant science · 2017Article
- Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved.PLoS computational biology · 2016Article
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- Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2011Article
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Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDispersed repeats are a major component of eukaryotic genomes and drivers of genome evolution. Annotation of DNA sequences homologous to known repetitive elements has been mainly performed with the program REPEATMASKER. Sequences annotated by REPEATMASKER often correspond to fragments of repetitive elements resulting from the insertion of younger elements or other rearrangements. Although REPEATMASKER annotation is indispensable for studying genome biology, this annotation does not contain much information on the common origin of fossil fragments that share an insertion event, especially where clusters of nested insertions of repetitive elements have occurred.
resultsHere I present REANNOTATE, a computational tool to process REPEATMASKER annotation for automated i) defragmentation of dispersed repetitive elements, ii) resolution of the temporal order of insertions in clusters of nested elements, and iii) estimating the age of the elements, if they have long terminal repeats. I have re-annotated the repetitive content of human chromosomes, providing evidence for a recent expansion of satellite repeats on the Y chromosome and, from the retroviral age distribution, for a higher rate of evolution on the Y relative to autosomes.
conclusionREANNOTATE is ready to process existing annotation for automated evolutionary analysis of all types of complex repeats in any genome. The tool is freely available under the GPL at http://www.bioinformatics.org/reannotate.
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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.