3.1 Display a pregenerated, static map

Static maps are pre-generated, non-interactive maps, which provide an overview of the syntenic relationships. Extensive datasets of virtual comparisons for each chromosome from rat, mouse and human exist as integral parts of VCMap build. In response to a search request (comprising of one backbone species and one of its chromosomes), the user can obtain 1 .a VCMap display of syntenic chromosomal segments from other two non-backbone species in almost a fixed (static) format and 2. mapped markers overlaid on these chromosomal segments. Being a static map, only a proportion of mapped markers can be displayed for any chromosomal interval.

To go to Static maps page, click on the link Static Maps on the left column of the VCMap Start page.

The “backbone” species is chosen from human, mouse or rat for which syntenic regions from other two species are queried. Upon clicking on one of its chromosomes, the VCMap generates a visual display of virtual comparative map with syntenic chromosomal segments and mapped markers.

Question: How do I interpret the static comparative maps?

Color code of the display consists of backbone species, non-backbone species, RH framework markers on the backbone, other mapped markers, and chromosome number above each syntenic chromosomal segment.

The result page has brief instructions, an option for viewing an expanded list of markers and the comparative map itself. By looking at the comparative map generated, the user can find out the possible syntenic chromosomal regions in non-backbone species compared to a whole chromosome from the backbone species. There are three ways to obtain marker details. They are:

a. Generate individual marker reports: The markers are hyperlinked to individual marker reports. Click on any marker to get a Query Result for that marker.

b. Generate chromosomal region reports: The chromosomal segments of the backbone species with definite breakpoints are differentially colored. By clicking on each segment, Chromosomal Region Report with expanded list of markers can be generated.

c. Search a specific chromosomal region: A table of expanded list of markers and VCMap predictions with in a specific chromosomal region can be generated. For this, enter the two flanking cR units from the generated map in the search fields and click GO.

For example, the VCMap result for such a query between 0.0 cR to 60.0cR for rat chromosome 1 backbone will look like:

Click to see result.

The marker reports have a clickable option to obtain MapView reports. The backbone species can be shuffled on a static map display by clicking on the hyperlinked blue chromosome numbers in the non-backbone species column.

3.2 Display dynamic maps using MapView?

Dynamic maps are highly interactive maps generated using MapView from the VCMap database in response to a specific user query. MapView can display multiple maps in a single window. The user can determine the types of maps to be compared and the features of the generated comparison to be displayed. The generated map has zoom option for the user to display the backbone markers in a specific region of comparison. The images are clickable to obtain the comparative data in the form of Query Pages.

To go to Dynamic Maps Page, click on MapView (Dynamic) link from the left side of the VCMap start page link. This will take the user to the MapView query page. Options for generating dynamic maps include:

a. Map data: Three kinds of Map data are available and the user can arrange these in any combination. Any combination of maps can be displayed for comparison.
Virtual syntenic maps The user can choose from rat, mouse and human. The version of VCMap build is 5.0_HS.
RH map options are varied for each species. For rat three versions are available while human and mouse have one standard version each.
Genetic maps from different sources are available for rat, mouse and human. Choose the appropriate build and version of the maps of choice.

b. VCMap predictions: If the user wants bin and stream predictions or framework markers, appropriate boxes are to be checked BEFORE the choices are submitted.

1. Querying virtual, genetic and RH maps: The Query interface for MapView is user friendly. The user is expected to choose
   - Single map or a map combination
   - A back bone species and 1 or 2 non-backbone species for each map option chosen a chromosome of the backbone species for the comparative analysis for each map option
2. Choosing prediction options
   User has an option to see the following VCMap predictions in different combinations directly on the map:
   Framework markers, Bin predictions and Stream predictions. The options are listed as:
   
   The options have to be chosen BEFORE the search parameters are submitted.

On submitting the search parameters, MapView loads the Java applet and the data first and opens a new browser window, which should be left open. The java display window will then appear with the maps specified by the user. The display window has multiple menu options on the top. These options can be used to fine-tune the map display.

1. How can I locate a marker on the generated map?
   To locate a marker on the map, go to Edit and choose Find. Enter the marker name in the query field. The user can arrive at this Find query from the map itself by clicking on the Find at the top right corner above the map.
   
2. How can I directly obtain the details of an alignment or a marker?
   By double-clicking an isolated marker or one in an alignment, Query Result can be obtained.
   
3. How can I display the details of the markers and VCMap predictions on the dynamic map?
   All the markers listed on the maps are clickable to generate ‘Individual Marker report’ or ‘Map report’.
   
4. How can be the VCMap predictions chosen by me displayed on the map?
   Once the map is generated, click on the Markers button at the top left of the page and make your choice from the list.
   
5. When Bin and Stream predictions are requested, the user has to click on Repack every time the scale is changed. This is because, by increasing or decreasing the resolution of the map, display of bin and stream predictions are also modified. Repack matches the display of the predictions to the scale of the displayed map.
   
6. 6. How can I modify the displayed maps in MapView?
   Zoom in and Zoom out: By sliding on the scale above the map the user can increase or decrease the resolution of the map. This is useful when the markers hidden in the static maps have to be visualized. By zooming out to the maximum, the resolution of the displayed map is increased to include all the available markers from the VCMap build.
   
7. What are the options for the marker display in a MapView map?
   By choosing different options available under View in the menu, characteristics of the displayed markers can be varied:
   
   Markers: under View by choosing Markers, the user has an option to choose:
   

   D-number : to obtain associated EST # if any
   Submitted: to obtain associated gene symbol
   Primary: to obtain Unigene/ UniSTS associated with that marker

   Marker Colors: under View by choosing Marker Colors, the user can provide different colors to the different marker types. A sliding scale is provided to expand the options of the colors.
   
   Show Markers: under View, by choosing Show Markers, the user can determine the type of markers and the priority for display.

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