The Genetic Map Comparator

A user friendly tool to compare and characterize genetic maps

2. Explore your data

using the top buttons to navigate through the proposed views

project leader: Yan Holtz

other project members: Vincent Ranwez & Jacques David

- Key Statistics (1 map) -

This table provides five key statistics for the chromosomes of the selected map: 1. their number of genetic markers, 2. their overall size (in cM), 3. the average gap size between 2 of their markers (cM), 4. the size of their biggest gap (cM) and the number of unique positions. This is the usual table you provide when doing a publication involving genetic maps.

- Key Statistics (several maps) -

Here you can compare various maps through five key statistics:

1. Number of genetic markers, 2. Overall size (in cM), 3. Average gap size between 2 of their markers (cM), 4. Size of their biggest gap (cM) and the number of unique positions.

The donut plot (on the left) summarizes the selected statistic comparison, whereas the bar-plot provides details for every chromosome separately.

- Marker Density -

Here is a description of marker density along chromosomes. This figure allows to visualize chromosome length variation among maps, and to identify regions with unusually high/low genetic marker density.

- Comparison of Marker Positions -

The main goal of this application is to compare genetic positions of markers from several genetic maps. Select maps in the order you want to see them (each new selected map is added on the right).

Common markers between two adjacent maps are linked with lines. Hover markers to get their names. You can also zoom on a specific area, and slide along the Y axis (position in cM). Double-click to come back to the initial view. You can personalize the rendering by choosing line thickness and colour.

The minimal subset of markers that would need to be removed to avoid crossing edges between 2 adjacent maps is detected and represented by grey lines. It is also possible to download the list of these markers.

Custom colors / font

- Interchromosome Analysis -

The comparison of marker positions can be observed for two maps. Selecting a single chromosome allows to visualize recombination rates between maps. Selecting all chromosomes allows to visualize interchromosome recombinations (i.e. markers not attributed to the same chromosome in the two maps)

Custom colors

Marker Information and Filtering

This table shows the raw marker data (as read from your input file) for the selected map. You can sort rows (i.e. markers) according to i) chromosome/group location, ii) name or iii) position. You can also search for a specific marker based on its name.

It is also possible to remove markers from the analysis. If you want to do so, please type the name of a marker to remove (e.g: ’sPb-601’) or a pattern to remove using regular expressions (e.g. typing ’sPb.*’ will remove all markers starting by sPb). If you want to remove several markers/patterns, separate them with a comma (e.g: ’sPb-601,xbarc-213’). You can also decide to keep only some markers, selecting the ‘keep’ option.
e.g. '.*25.*'

- About -

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 ‘Home’ 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.

- Input Files -

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 ‘;’ 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

- Run the Application Locally -

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:

- 3/ Call the application from its Github repository typing this command in the R console:

Sharing published maps

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.

- Contact -

Yan Holtz: Vincent Ranwez:

Ge2pop Team, Bâtiment 21
Montpellier SupAgro,
2 place Pierre Viala
34060 MONTPELLIER Cedex 1

- References -

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.