ArkDB Map Drawing

Select a Species

ArkDB provides map selection and drawing opportunities at various logical points in the application. An alternative pathway to drawing maps is provided by the Simple Maps Interface


What to do here:

Go to the ArkDB Home Page

Select a Species from the ArkDB Species icons


Select a Chromosome

The list of chromosomes is graphically displayed.


What to do here:

Click on the species chromosome of interest


Select a Map

The available map types for this species chromosome are displayed:

  • Cytogenetic Map
  • Linkage Maps
  • Linkage Maps with QTL Mappings
  • Radiation Hybrid Maps
  • Composite Maps
  • Contig Maps
  • Sequence Maps


    • What to do here:

    To draw Maps:-

    Select one or more maps by checking (ie clicking on) the individual checkboxes for each map name

    Alternatively click on the 'Select All Maps' button to checkbox ALL maps

    Click the 'Draw Maps' button

    or:-

    to see 'Marker Details' for a map:-

    Click on the map name


    Map Drawing Application

    The users selected maps are drawn by the map drawing application. Map names, locus details and map relationships are displayed. Map drawing functionality provides further scope to perform operations like Zoom,Flip and Move.

    What to do here:

    See the map drawing application tutorial for functional details


    Map DetailsIf the user chose to display map details, then the list of markers and their positions are displayed. The user can continue onwards to draw the Map or can click on any marker to determine whether there are other related ArkDB maps which contain these markers - drawing them will demonstrate that relationship.

    What to do here:

    To draw the Map:-

    Click the 'Draw Map' button

    or:-

    To find related maps (common markers):-

    Click on the Marker Name


    Marker Details

    If the user chose to display marker details for a map, then these are displayed. These details include:

  • Name
  • Type
  • Pubmed Publication ID
  • Primers
  • Related Sequences
  • Related Markers
  • Related Maps

    • Note: the related maps are those ArkDB maps which contain this same marker. These maps can be selected by clicking on the checkbox for each related map. When drawn, this marker relationship is visible by virtue of relationship lines which join the common markers.

    What to do here:

    Click on the checkbox for each Map

    or:-

    Click on the 'Select All Maps' button to checkbox all related Maps

    Click the 'Draw Maps' button


    Points to be aware of:

  • Navigating and altering selection criteria. The browser's 'Back' arrow button takes the SimpleMaps interface back to the preceeding page. In this way its possible to correct an error in map selection criteria. "Oops - I'm on the 'which mapping Analysis' page ...but I actually meant to select Maps for Chicken-Turkey-Duck, not for Chicken-Turkey-Quail". Browser 'Back' button will take the interface back to the point where the selection can be changed. In this way selection criteria can be altered all the way back - even to the start of the SimpleMaps interface eg decide to select 6 Maps rather than 4.

  • Initialising selection criteria. An effective way to completely reset the selection criteria at any time, is just to click 'Maps' in the ArkDB menu bar. The effect of this is to reset the SimpleMaps criteria right back to their opening "non user specified" values.

  • If maps don't draw. If selected maps don't display in the map drawing application, then there are "known issues" which may account for this. Consult the ArkDB help page for a current list of these known issues which could affect the capability of the map drawing application.