Conserved Segment View Plugin

Contents

1. Description
2. Usage by Example
3. Special Tips
4. Config Tree

Description

Fig. 1	Fig. 2

Usage by Example

1. File -> Load, open the file "inparanoidTax9606Tax10090.tree"
   
2. Plugins -> Conserved Segment View. A window called "Conserved Segment View Control" will appear, usually in the upper-left corner of your screen.

   Fig. 3

   
   
3. Double-click on "Synteny Mapping #1", then a window called "ConservedSegmentView - Synteny Mapping #1" will appear. This window will display all conserved segment pairs. Use Scale Down and Scale Up buttons to adjust segments to feasible sizes.

   Fig. 4

   
   
4. Back to GOBU window, click user node "User Data", then all locations are marked on conserved segment pairs. Orthologous objects in same conserved segment pair will be connected by a gray line.
   
5. Check Marked only box (i.e. ensure this option is selected), click unit user node "gropu13639", then all previously marked locations are removed and locations (i.e. LOC P-nodes) under gropu13639 are newly marked. Because un-marked conserved segment pairs will be removed if Marked only is checked, there will be only one conserved segment pair in the ConservedSegmentView window.
   
6. Move mouse cursor to "(106105001,107785001)@chr11@Mouse" or "(61025001,63095001)@chr17@Human" and stop for a while, a tool tip will appear. This tool tip tells the ID (ConserveSegment238) of this conserved segment pair.
   
7. Check Additive box, select a new color in Use color list, then click user node "User Data". Scroll ConservedSegmentView window so that you can see ConserveSegment238. You will see group13639 LOC P-nodes are marked by two colors (Fig. 5, blue circle). group13639 LOC P-nodes will not be removed because checked Additive option ensures the additive drawing.

   Fig. 5

   
   
8. Click Remember button. Every time you click this button, marked locations will be remembered with their assigned colors.
   
9. Select a third color in Use color list, un-check Live box (i.e. ensure this option is un-selected), click any user node, then nothing happens in the ConservedSegmentView window. This is because un-checked Live option lets ConservedSegmentView window not to response to user selections immediately.
   
10. Ensure user node "group233" is selected, mouse-right-click, select "Conserved Segment Drawing", then group233 LOC P-nodes are marked by the third color. (group 233 locations are also in ConserveSegment238)
    
11. Click first Clear button (the one next to Scale Up button), then you will find that only third color markers are cleared. This is because markers of first two colors are remembered.
    
12. Double-click somewhere around gropu13639 locations, an enlarged view window called "1 - ConservedSegmentView - Synteny Mapping #1" will appear. Note that a pair of blue dash-line boxes will appear on ConserveSegment238 for indicating the corresponding region of the enlarged view window. In the case that you have multiple enlarged view windows, the numbers appended to blue dash-line boxes and the numbers appended to their window titles will show the correspondence (see Fig. 6, blue and red circle).

    Fig. 6

    
    
13. Move mouse cursor to the edge of enlarged view window, drag (i.e. hold mouse-lef-button and move mouse) to resize window. By widening enlarged view window, you will see the size of corresponding blue dash-line boxes is changed.
    
14. The upper coordinate shows the chromosomeal position of first segment, doule-click on it to re-center the enlarged view (i.e. movements of enlarged view region). Try centering your enlarged view to 107280K base-pair.
    
15. Scale Down or Scale Up so that you see first segment from 107120K to 107480K.
    
16. Drag mouse accross two segment bands and from 107120K to 107480K, a popup menu with two items (label and de-label) will appear (see Fig. 7), then select label. You will find that locations in dragged region will be labeled with their names, i.e. the node names of corresponding R-nodes (see Fig. 8. In this case, node names are refseq protein GIs). For locations assigned with two colors, their labels will be followed by two colored squares. For locations assigned with one colors, their labels will be followed by one colored square.

    Fig. 7	Fig. 8

    
    
17. Move mouse cursor around the enlarged view window and stop for a while, a tool tip will appear.

    Fig. 9

    • Upper coordinate: "double click to re-center"
    • Location boxes: corresponding label name and "double-click to label"
    • Colored squares: corresponding information in user tree (the path infomation of this label, i.e. R-node) and "double-click to goto"
    • Lower coordinate: "mouse drag on coordinate for shift"
    Drag mouse along lower coordinate, from 62320K to 62080K, then second segment will be shifted. This function may help observing ortholog arrangement.
    
18. Click second Clear button (the one next to Remember button), click first Clear button, then you will find that all LOC P-nodes are cleared. Second Clear button is for releasing all remembered locations.
    
19. Check Live and Marked only, un-check Additive, set Appearance level of user tree to Unit, then click on any GO node. The drawn locations should belong to selected R-nodes, i.e. R-nodes of selected unit nodes.

Special Tips

1. Check Live, Additive and Marked only, set Appearance level of user tree to Unit, then select Search -> Search GO tree. You may input your desired search pattern and options, you will see all related locations of groups by clicking Iterate all button.

Config Tree

This plugin obtains synteny mapping configurations from config tree. Descendant SyntenyConfig P-nodes of Synteny Mapping Configurations P-node represent synteny mapping configurations. Under each SyntenyConfig P-node, we advise you to use R-nodes to represent conserved segment pairs. In each conserved segment pairs, you must use two LOC P-nodes to represent the two conserved segment, also use a normal node of the form direction:<forward or reverse> to represent the mapping direction.

See files "synteny1.tree" and "synteny2.tree" in config sub-folder for examples.