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dc.contributor.authorTan, Ge
dc.contributor.authorPolychronopoulos, Dimitris
dc.contributor.authorLenhard, Boris
dc.PublishedTan G, Polychronopoulos D, Lenhard B. CNEr: A toolkit for exploring extreme noncoding conservation. PLoS Computational Biology. 2019;15(8):1-16eng
dc.description.abstractConserved Noncoding Elements (CNEs) are elements exhibiting extreme noncoding conservation in Metazoan genomes. They cluster around developmental genes and act as long-range enhancers, yet nothing that we know about their function explains the observed conservation levels. Clusters of CNEs coincide with topologically associating domains (TADs), indicating ancient origins and stability of TAD locations. This has suggested further hypotheses about the still elusive origin of CNEs, and has provided a comparative genomics-based method of estimating the position of TADs around developmentally regulated genes in genomes where chromatin conformation capture data is missing. To enable researchers in gene regulation and chromatin biology to start deciphering this phenomenon, we developed CNEr, a R/Bioconductor toolkit for large-scale identification of CNEs and for studying their genomic properties. We apply CNEr to two novel genome comparisons—fruit fly vs tsetse fly, and two sea urchin genomes—and report novel insights gained from their analysis. We also show how to reveal interesting characteristics of CNEs by coupling CNEr with existing Bioconductor packages. CNEr is available at Bioconductor ( and maintained at github (
dc.rightsAttribution CC BYeng
dc.subjectDrosophila melanogastereng
dc.subjectInvertebrate genomicseng
dc.subjectMammalian genomicseng
dc.subjectSequence alignmenteng
dc.subjectGenetic locieng
dc.titleCNEr: A toolkit for exploring extreme noncoding conservationeng
dc.typeJournal articleeng
dc.typePeer reviewedeng
dc.rights.holderCopyright 2019 Tan et al.eng
dc.source.journalPLoS Computational Biology

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