ArticleBioinformatics (Oxford, England)2010
Cassis: detection of genomic rearrangement breakpoints.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Pangenome comparison via ED strings.Frontiers in bioinformatics · 2024Article
- Comparative genome analysis of the freshwater fungus Filosporella fistucella indicates potential for plant-litter degradation at cold temperatures.G3 (Bethesda, Md.) · 2023Article
- Genomic insights into the host specific adaptation of the Pneumocystis genus.Communications biology · 2021Article
- Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps.BMC biology · 2020Article
- A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution.Genome biology and evolution · 2018Article
- Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.Genome research · 2017Article
- Recombination rate variation in mice from an isolated island.Molecular ecology · 2017Article
- Refining borders of genome-rearrangements including repetitions.BMC genomics · 2016Article
- Advances in computer simulation of genome evolution: toward more realistic evolutionary genomics analysis by approximate bayesian computation.Journal of molecular evolution · 2015Article
- A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution.Molecular ecology · 2014Article
- An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae.BMC genomics · 2014Article
- Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions.BMC genomics · 2014Article
- Evaluating synteny for improved comparative studies.Bioinformatics (Oxford, England) · 2014Article
- Recombination rates and genomic shuffling in human and chimpanzee--a new twist in the chromosomal speciation theory.Molecular biology and evolution · 2013Article
- Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution.BMC bioinformatics · 2012Article
- Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny.BMC genomics · 2011Article
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6 authors.
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Abstract
summaryGenomes undergo large structural changes that alter their organization. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. Lemaitre et al. presented a new method to precisely delimit rearrangement breakpoints in a genome by comparison with the genome of a related species. Receiving as input a list of one2one orthologous genes found in the genomes of two species, the method builds a set of reliable and non-overlapping synteny blocks and refines the regions that are not contained into them. Through the alignment of each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Here, we present the package Cassis that implements this method of precise detection of genomic rearrangement breakpoints. AVAILABILITY: Perl and R scripts are freely available for download at http://pbil.univ-lyon1.fr/software/Cassis/. Documentation with methodological background, technical aspects, download and setup instructions, as well as examples of applications are available together with the package. The package was tested on Linux and Mac OS environments and is distributed under the GNU GPL License.
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