ArticleNucleic acids research2010
Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed).BMC bioinformatics · 2024Article
- Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish.International journal of molecular sciences · 2023Article
- Slaying (Yet Again) the Brain-Eating Zombie Called the "Isochore Theory": A Segmentation Algorithm Used to "Confirm" the Existence of Isochores Creates "Isochores" Where None Exist.International journal of molecular sciences · 2022Article
- Genome-wide oscillations in G + C density and sequence conservation.Genome research · 2021Article
- OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes.Genome biology and evolution · 2016Article
- Segmenting the Human Genome into Isochores.Evolutionary bioinformatics online · 2015Article
- A comparative study and a phylogenetic exploration of the compositional architectures of mammalian nuclear genomes.PLoS computational biology · 2014Article
- Investigating genomic structure using changept: A Bayesian segmentation model.Computational and structural biotechnology journal · 2014Review
- Finding the missing honey bee genes: lessons learned from a genome upgrade.BMC genomics · 2014Article
- Article
- Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid.Nucleic acids research · 2014Article
- IsoPlotter(+): A Tool for Studying the Compositional Architecture of Genomes.ISRN bioinformatics · 2013Article
- The GenoChip: a new tool for genetic anthropology.Genome biology and evolution · 2013Article
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4 authors.
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Abstract
It has been suggested that the mammalian genome is composed mainly of long compositionally homogeneous domains. Such domains are frequently identified using recursive segmentation algorithms based on the Jensen-Shannon divergence. However, a common difficulty with such methods is deciding when to halt the recursive partitioning and what criteria to use in deciding whether a detected boundary between two segments is real or not. We demonstrate that commonly used halting criteria are intrinsically biased, and propose IsoPlotter, a parameter-free segmentation algorithm that overcomes such biases by using a simple dynamic halting criterion and tests the homogeneity of the inferred domains. IsoPlotter was compared with an alternative segmentation algorithm, D(JS), using two sets of simulated genomic sequences. Our results show that IsoPlotter was able to infer both long and short compositionally homogeneous domains with low GC content dispersion, whereas D(JS) failed to identify short compositionally homogeneous domains and sequences with low compositional dispersion. By segmenting the human genome with IsoPlotter, we found that one-third of the genome is composed of compositionally nonhomogeneous domains and the remaining is a mixture of many short compositionally homogeneous domains and relatively few long ones.
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