The Genetic Map Comparator allows to easily compare several linear maps (genetic, physical, radiated hybrids). The first step is to upload your maps through the Select Dataset sheet. Three example datasets (from sorghum and wheat) are provided to easily explore the Genetic map comparator features. For a more in depth analysis of your genotyping data (He, FIS, MAF, ..), you may find
SNiPlay
[1] useful.
Once a dataset is uploaded you can explore it using the various sheets accessible via links at the top of the window. Each sheet helps you to study some specific features of your maps, they allow you to compare your maps via standard statistics (number of markers, average gap size between markers etc.) as well as to obtain a visual representation of your map congruences by plotting marker positions along chromosomes.
The Genetic map comparator is able to import map files produced by most commonly used software for linkage analysis (e.g. Carthagene and JoinMap). Each map must be stored in its own file and all data files stored together in one specific folder. Use the upload facility of the home page to browse your local folders and select desired maps using multiple file selection. The column name has no impact but must be ordered correctly (see details and example below) and be separated by either semi-colon (;) or tabulation (\t). Three formats are accepted:
OneMap
[2] format: 3 columns: linkage group, marker name and position in the map.
Download
MapChart
[3] format: composed of a sequence of linkage groups, each with a header specifying the linkage group title, followed by a sequence of lines with locus names and map positions.
Download
Carthagène
[4] format: 1 line only. Linkage groups are separated with {}. Then marker names and positions are provided successively. Output created with the 'mapget' command.
Download
The Genetic Map Comparator is an R shiny application available online. Uploaded data are NOT kept on the Webserver. However, for confidentiality or better reactivity, it is also easy to run it locally following these steps:
- 1/
Install R
on your computer and open it.
- 2/ Install the R Shiny library. In the R console type the following commands:
install.packages(shiny)
library(shiny)
- 3/ Call the application from its Github repository typing this command in the R console:
runGitHub("GenMap-Comparator","holtzy")
see also the
geneticMapComparator github repository
Uploaded data are NOT kept on the Webserver, but if you want to share your published data with the community via this Genetic Map Comparator website, please do not hesitate to contact us. We will be glad to add your maps on the list of proposed maps displayed on the home page.
Vincent Ranwez: ranwez@supagro.fr
Ge2pop Team, Bâtiment Arcad
10 rue Arthur Young
34090 MONTPELLIER, FRANCE
1. Dereeper A., Nicolas S., Lecunff L., Bacilieri R., Doligez A., Peros JP., Ruiz M., This P. SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.. BMC Bioinformatics. 2011. May 5;12(1):134.
2. Margarido GRA, Souza AP, Garcia AAF. OneMap: software for genetic mapping in outcrossing species. Hereditas. Wiley Online Library; 2007;144: 78–79.
3. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, et al. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics. Elsevier; 1987;1: 174–181.
4. de Givry S, Bouchez M, Chabrier P, Milan D, Schiex T. CARTHAGENE: Multipopulation integrated genetic and radiation hybrid mapping. Bioinformatics. 2005;21: 1703–1704.