ArticleF1000Research2018
segment_liftover : a Python tool to convert segments between genome assemblies.
Article in F1000Research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Progenetix oncogenomic resource in 2021.Database : the journal of biological databases and curation · 2021Pooled it
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- Comprehensive analysis of H3K27me3 LOCKs under different DNA methylation contexts reveal epigenetic redistribution in tumorigenesis.Epigenetics & chromatin · 2025Article
- cancercelllines.org-a novel resource for genomic variants in cancer cell lines.Database : the journal of biological databases and curation · 2024Article
- Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues.Genome biology · 2023Article
- Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster.PLoS genetics · 2023Article
- Potential mechanisms and prognostic model of eRNAs-regulated genes in stomach adenocarcinoma.Scientific reports · 2022Article
- Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals.Journal of molecular evolution · 2022Article
- Article
- CloneSig can jointly infer intra-tumor heterogeneity and mutational signature activity in bulk tumor sequencing data.Nature communications · 2021Article
- Comparative genomic analysis of a naturally born serpentized pig reveals putative mutations related to limb and bone development.BMC genomics · 2021Article
- Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes.Frontiers in genetics · 2021Article
- Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data.NAR genomics and bioinformatics · 2020Article
- RBP EIF2S2 Promotes Tumorigenesis and Progression by Regulating MYC-Mediated Inhibition via FHIT-Related Enhancers.Molecular therapy : the journal of the American Society of Gene Therapy · 2020Article
- SuperFreq: Integrated mutation detection and clonal tracking in cancer.PLoS computational biology · 2020Article
- Assessing reliability of intra-tumor heterogeneity estimates from single sample whole exome sequencing data.PloS one · 2019Article
- Utility and First Clinical Application of Screening Embryos for Polygenic Disease Risk Reduction.Frontiers in endocrinology · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The process of assembling a species' reference genome may be performed in a number of iterations, with subsequent genome assemblies differing in the coordinates of mapped elements. The conversion of genome coordinates between different assemblies is required for many integrative and comparative studies. While currently a number of bioinformatics tools are available to accomplish this task, most of them are tailored towards the conversion of single genome coordinates. When converting the boundary positions of segments spanning larger genome regions, segments may be mapped into smaller sub-segments if the original segment's continuity is disrupted in the target assembly. Such a conversion may lead to a relevant degree of data loss in some circumstances such as copy number variation (CNV) analysis, where the quantitative representation of a genomic region takes precedence over base-specific accuracy.
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