ArticleGenome research2009
Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Efficient algorithms for simulating sequences along a phylogenetic tree.Bioinformatics (Oxford, England) · 2026Article
- A wavelet-based approach generates quantitative, scale-free and hierarchical descriptions of 3D genome structures and new biological insights.PLoS computational biology · 2026Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions.Molecular biology and evolution · 2021Article
- Assessing Autosomal InDel Loci With Multiple Insertions or Deletions of Random DNA Sequences in Human Genome.Frontiers in genetics · 2021Article
- Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse.PLoS computational biology · 2018Article
- Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans.BMC evolutionary biology · 2017Article
- Application of discrete wavelet transform for analysis of genomic sequences of Mycobacterium tuberculosis.SpringerPlus · 2016Article
- Purifying Selection Maintains Dosage-Sensitive Genes during Degeneration of the Threespine Stickleback Y Chromosome.Molecular biology and evolution · 2015Article
- Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders.Journal of molecular evolution · 2015Article
- Hellbender genome sequences shed light on genomic expansion at the base of crown salamanders.Genome biology and evolution · 2014Article
- Precise estimates of mutation rate and spectrum in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels.Genome biology · 2013Article
- Microsatellite-based evidences of genetic bottlenecks in the cryptic species "Andrographis paniculata Nees": a potential anticancer agent.Molecular biology reports · 2013Article
- Slow DNA loss in the gigantic genomes of salamanders.Genome biology and evolution · 2012Article
- An exonic insertion within Tex14 gene causes spermatogenic arrest in pigs.BMC genomics · 2011Article
- Genome analyses substantiate male mutation bias in many species.BioEssays : news and reviews in molecular, cellular and developmental biology · 2011Review
- Review
- A time-invariant principle of genome evolution.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains.Nucleic acids research · 2010Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Recent studies have revealed that insertions and deletions (indels) are more different in their formation than previously assumed. What remains enigmatic is how the local DNA sequence context contributes to these differences. To investigate the relative impact of various molecular mechanisms to indel formation, we analyzed sequence contexts of indels in the non protein- or RNA-coding, nonrepetitive (NCNR) portion of the human genome. We considered small (<or=30-bp) indels occurring in the human lineage since its divergence from chimpanzee and used wavelet techniques to study, simultaneously for multiple scales, the spatial patterns of short sequence motifs associated with indel mutagenesis. In particular, we focused on motifs associated with DNA polymerase activity, topoisomerase cleavage, double-strand breaks (DSBs), and their repair. We came to the following conclusions. First, many motifs are characterized by unique enrichment profiles in the vicinity of indels vs. indel-free portions of the genome, verifying the importance of sequence context in indel mutagenesis. Second, only limited similarity in motif frequency profiles is evident flanking insertions vs. deletions, confirming differences in their mutagenesis. Third, substantial similarity in frequency profiles exists between pairs of individual motifs flanking insertions (and separately deletions), suggesting "cooperation" among motifs, and thus molecular mechanisms, during indel formation. Fourth, the wavelet analyses demonstrate that all these patterns are highly dependent on scale (the size of an interval considered). Finally, our results depict a model of indel mutagenesis comprising both replication and recombination (via repair of paused replication forks and site-specific recombination).
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Registered trials
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