1. This tutorial will describe how to navigate the section of Gramene that allows you to view various types of maps (e.g., genetic, physical, or sequence-based) from different species and construct comparisons between them. CMap was originally written for the Gramene project (http://www.gramene.org/) and is now part of the GMOD (Generic Model Organism Database) Project (http://www.gmod.org/).http://www.gramene.org/http://www.gmod.org/ Welcome to the Comparative Map Viewer (CMap) Tutorial.

2. CMap Menu Select to link to the Feature Search (See Slides 23-25 for more info). Select to view more info on the Feature Types (See Slide 36). Select to view more info on the Species that are represented (See Slide 39). Select to link to the Map Viewer (See Slides 5-22 for more info). Select to link to the Correspondence Matrix (See Slides 26-33 for more info). Select to view more info on the Evidence Types (See Slide 38). Select to view more info on the Map Types (See Slide 37). Select to view more info on the Map Sets (See Slides 34-35).

3. Entering CMap There are three main entry points to viewing maps in CMap: 1)Comparative map viewer: Choose a starting map and add comparative maps to the right or left (See Slides 5-22). 2)Feature search: Search for a particular feature by name, accession ID, species, or feature type (See Slides 23-25). 3)Correspondence matrix: View the number of correspondences among all maps and choose a pair to display in the viewer; continue by adding more comparative maps (See Slides 26-33).

4. Comparative Map Viewer Choose “All” or one species to display in “Ref. Species.” Quick start instructions

5. Comparative Map Viewer If the Ref. Species is limited to rice, only rice map sets appear in the Ref. Set drop-down menu. They are grouped by map types (sequence, genetic, etc). Select a map set and click “Submit.”

6. Comparative Map Viewer Select a Ref. Map from the drop-down menu. Information on the Ref. Set will appear when one is selected.

7. Reference map Map legend Menu Resulting Reference Map

8. Glyphs box dumbbell line span up-arrow down-arrow double-arrow filled-box in-triangle out-triangle The following demonstrate all the glyphs (shapes) that map features could appear as.

9. Reference Map Image with all* features shown and labeled. * “all” meaning “all that will fit.” If a desired feature is not shown, you can enter it in the “Highlight” field (See Slide 13). Map coordinate Glyphs showing feature locations. Select any of the features to view its “Feature Details” Page (See Slide 25). Feature labels in same color as glyph Map units

10. Map Menu on Reference Map Species name Map set name Map name Select to view this particular “Map Set Info.” Select to view the “Map Details” (See Slides 20-22). Select to “Flip” map. This option allows correspondence lines between two maps to align better. Select to make a new view with this map, which allows for comparison with other maps.

11. Map Legend Listing of all the feature types found on the map with their corresponding glyphs Description of menu buttons Select to link to the Generic Model Organism Database (GMOD) /CMap homepage.

12. Customizing the Comparative Map Viewer * Highlight using either the feature’s name, an alias, or the feature’s accession ID. The “Start” & “End” fields allow for changing the size of the region shown. The “Highlight” field allows for highlighting any feature on the map.* The “Comp. Map” fields allow for positioning other maps to the right or left (See Slide 17). The Drawing Options fields allow you to change the “look” of the map (See Slides 14-16). The “Correspondence Type” field allows restriction of correspondences by evidence type. Select “Show Map” to submit choices.

13. Drawing Options in the Map Viewer Determines which feature labels will be shown on the map Allows you to select the type of image Determines the size of the font Determines the vertical height of the image

14. This options determines whether to use one glyph for features that span over the same coordinates or to repeat the glyph for each feature. Collapsed Not collapsed Drawing Options in the Map Viewer

15. Allows you to determine the minimum number of correspondences that are desired from map to map. Determines which feature types to include on the maps. If no selection is made, all feature types are included.

16. “Comp. Map” fields in the Map Viewer You may place maps for comparison on the left and right of the reference map (and continuing on, ad infinitum). Choose one or all of the maps from this set. The number in the square brackets indicates the number of correspondences to the reference map.

17. Adding Comparative Maps Pictured here is the reference map (Rice-JRGP-1) in the middle with a QTL map on its left and a genetic map on its right. Features with correspondences appear in red (noted in legend) Lines show correspondences. The color of the line denotes evidence type (noted in legend). When multiple evidences support a correspondence, the one with the highest rank is used to color the line.

18. Choosing “Landmarks” in the “Show Labels” field shows only features tagged as “landmarks” and features with correspondences, reducing the clutter of extra labels.

19. Map Details Table Clicking on the ? button in the map menu will display a Map Details Table. The table contains details of every feature on the reference map, including the feature’s name, type, position, and all its correspondences. Select to view the data in the table in a tab- delimited format.

20. Map Details Table You can restrict the correspondence information in the table to a particular map or map set. Choose a map or map set from the “Restrict by Map” field at the top of the table.

21. Map Details Table Select “View Maps” to see the reference map and this comparative map in the Map Viewer with the feature correspondence highlighted. Select on the feature names to view the “Feature Details” page (See Slide 25).

22. Feature Search To search for a feature, click on the “Search” link in the CMap menu. Choose a species (optional) Indicate the feature name(s) you wish to search for Choose a feature type (optional) Search either the feature’s name (and aliases) or accession ID

23. Feature Search Results Found 7,498 features with a name or alias matching “rm*” Click on the column title to view a sorted display list. Select to view the “Map Set Info” page (See Slides 34-35). Select to view this feature highlighted on this map Select to view the “Feature Details” Page for this feature

24. Feature Details Page This page displays a feature’s accession ID, type, name, any aliases, its map and location as well as any applicable attributes or cross-references assigned by the curator. In addition, all the correspondences are displayed in a table. Follow links to detail pages. Selecting “Show Maps” will display a comparison of the feature detail map (above) to this map. Both features will be highlighted. Select an evidence type to view the “Evidence Type Info” page (See Slide 38).

25. Correspondence Matrix The matrix is a cross-tabulated table showing the number of correspondences among all the map sets. When you first visit the matrix, you will be prompted to restrict the reference maps (the rows) by map type and/or species as the table can be quite large. To view the correspondence matrix, click on the “Matrix” link in the CMap menu. Select a map type and/or species. Click “Submit”

26. Correspondence Matrix After choosing a map type and/or species, the matrix will display all the correspondences from all the map sets which can act as reference maps to all the other map sets in CMap. Matrix restricted to “Barley” map sets Click on a map set name to restrict to just the maps in that set.

27. Correspondence Matrix When only one reference set is selected, the individual maps are displayed. Clicking on a number in the cell will take you to the Map Viewer showing the comparison of the map to all the maps of the comparative set. Here the reference set column has been limited to just one set.

28. Correspondence Matrix When multiple reference sets are displayed, clicking on a number in this view will restrict the matrix to just the maps in these two map sets.

29. Correspondence Matrix When both the reference and comparative maps sets are limited to one, clicking on a number in the matrix will take you to the Map Viewer showing a comparison of just two maps from each set. Here both the reference and comparative sets have been limited to just one set showing map-to-map correspondences.

30. Correspondence Matrix When the reference set is limited to just one set and the comparative maps (the top row) is restricted to one relational map set, the number of correspondences from the individual reference maps to all the maps of the comparative set are shown (i.e., the individual maps of the comparative set are not shown).

31. Correspondence Matrix Clicking on a comparative map set in the top row will restrict the top row to just that set.

32. Correspondence Matrix Here the comparative maps (in the top row) have been limited to just one map set. Clicking the number in this view will additionally break down the matrix map-by-map.

33. Map Set Info This page contains information on all the map sets, including their species, map type, names (“short” and “long”), any additional attributes the curator has assigned (e.g., “Description”), the names of the maps in the set (for non-relational maps) with links to view those maps (or “all”) in the viewer, and the feature types occurring on the maps in the set. There can be many map sets on the page, so you can restrict the sets with the controls at the top of the page. Choose a species and/or a map type to restrict the search. To view the “Map Set Info” page, click on the “Map Sets” link in the CMap menu.

34. Map Set Info A link to the map set in the Map Viewer A link to the “Species Info” page for this species (See Slide 39). A link to view the map(s) in the Map Viewer A link to view the “Feature Type Info” page for each feature type in this map set

35. Feature Type Info This page shows all the feature types used to classify the map features in CMap. Each feature type has a name, a color and a shape. The curator may additionally assign other attributes (such as a “Description”) and cross- references. To view the “Feature Type Info” page, click on the “Feature Types” link in the CMap menu.

36. Map Type Info To view the “Map Type Info” page, click on the “Map Types” link in the CMap menu. This page displays all the map types used to classify the maps in CMap. Each map type has a name, an accession ID, the map units used for maps of this type (e.g. “bp” for “base pair” or “cM” for “centimorgans”), an indication as to whether maps of this type are “relational,” and an indication of how maps of this are normally drawn (though this can be overridden at the map set level).

37. Correspondence Evidence Info To view the “Correspondence Evidence” page, click on the “Evidence Types” link in the CMap menu. This page contains the name of each evidence type used to support the correspondences in CMap. Each evidence has an accession ID, a rank relative to the other evidence types, and an assigned color for the line drawn on the map to differentiate the correspondence.

38. Species Info To view the “Species Info” table, click on the “Species” link in the CMap menu. This page contains the species’ common and full names along with any other attributes and cross- references the curators have created.

39. Thank you for using this tutorial. We appreciate any comments or suggestions. Please click here to send your feedback. http://www.gramene.org/db/feedback/send_feedback