CytoConverter: a web-based tool to convert karyotypes to genomic coordinates

BMC Bioinformatics

Janet Wang¹  Thomas LaFramboise¹ 

[1] Department of Genetics and Genome Sciences, Case Western Reserve University;

关键词: Cytogenetics;    Chromosomal abnormalities;    Karyotypes;    Text parsing;   

DOI  :  10.1186/s12859-019-3062-4

来源: DOAJ

【 摘 要 】

Abstract Background Cytogenetic nomenclature is used to describe chromosomal aberrations (or lack thereof) in a collection of cells, referred to as the cells’ karyotype. The nomenclature identifies locations on chromosomes using a system of cytogenetic bands, each with a unique name and region on a chromosome. Each band is microscopically visible after staining, and encompasses a large portion of the chromosome. More modern analyses employ genomic coordinates, which precisely specify a chromosomal location according to its distance from the end of the chromosome. Currently, there is no tool to convert cytogenetic nomenclature into genomic coordinates. Since locations of genes and other genomic features are usually specified by genomic coordinates, a conversion tool will facilitate the identification of the features that are harbored in the regions of chromosomal gain and loss that are implied by a karyotype. Results Our tool, termed CytoConverter, takes as input either a single karyotype or a file consisting of multiple karyotypes from several individuals. All net chromosomal gains and losses implied by the karyotype are returned in standard genomic coordinates, along with the numbers of cells harboring each aberration if included in the input. CytoConverter also returns graphical output detailing areas of gains and losses of chromosomes and chromosomal segments. Conclusions CytoConverter is available as a web-based application at https://jxw773.shinyapps.io/Cytogenetic__software/ and as an R script at https://sourceforge.net/projects/cytoconverter/. Supplemental Material detailing the underlying algorithms is available.

【 授权许可】

Unknown