Installing and Configuring CMap
互联网
522
- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
CMap is a Web?based tool for viewing comparisons between biological maps of different types. It allows for correspondences to be displayed between maps as disparate as genetic and physical maps. The protocols in this unit comprise a guide to installing, configuring, and importing data into CMap.
Keywords: CMap; comparative mapping; display
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryTable of Contents
- Basic Protocol 1: Getting Started with CMap
- Basic Protocol 2: Creating the CMap Database
- Basic Protocol 3: Configuring CMap
- Basic Protocol 4: Creating and Importing Data
- Basic Protocol 5: Advanced Configuration and Data Manipulation Options
- Support Protocol 1: Installing CMap
- Commentary
- Figures
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryMaterials
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryFigures
-
Figure 9.8.1 CMap image of comparison between a physical map and a genetic map. The lines between the maps are correspondences that point to the feature location on each map. The features in red are involved in the displayed correspondences. View Image -
Figure 9.8.2 The maps selection menu. Initially, only the Ref. Species and Ref. Set drop‐down boxes are displayed. The remaining options appear when a reference set is selected. These options allow for a more refined view. View Image -
Figure 9.8.3 Chromosome 1 from a rice sequence assembly. The features are drawn, according to the feature type configuration, as variously colored glyphs to differentiate themselves from each other. Various navigation buttons are present, including truncation arrows and menu icons. The map and features are also links which can be configured. View Image -
Figure 9.8.4 The Map Options menu with one reference map. Clicking the Add Maps Left and Add Maps Right links in the corners will bring up the comparative maps menu which allows for selection of the next corresponding maps. View Image -
Figure 9.8.5 The Comparative Maps menu. This menu is where the next corresponding maps are chosen. A minimum number of correspondences can be entered to limit the maps to those with a high number of correspondences. View Image -
Figure 9.8.6 Chromosome 1 of a sequence assembly compared to chromosome 1 of a genetic map set. The gray lines represent correspondences between features on these maps. The crossing correspondences indicate that these maps are not oriented correctly. View Image -
Figure 9.8.7 Maps from Figure with the genetic map flipped. Note the F (flip) icon above the genetic map is now UF (un‐flip). The correspondences are less tangled, and the image is more clear. View Image -
Figure 9.8.8 The maps selection menu after adding a correspondence map. The reference map options are in blue while the other map options are in white. As more corresponding maps are added, this table will reflect that growth. View Image -
Figure 9.8.9 The Feature Options menu. This menu allows for individual feature types to be treated differently. Some can be always displayed, while others can be only displayed if they are being used in a correspondence and still others can be ignored completely. Highlight Features will highlight the labels of the features with names written in the box. The options Show Labels and Collapse Overlapping Features affect how the image is drawn. View Image -
Figure 9.8.10 Tab delimited files used to import data into CMap. The first line in the file is the column headers. For an exhaustive list of possible fields, execute perldoc Bio::GMOD::CMap::Admin::Import. View Image -
Figure 9.8.11 The matrix entry point into the CMap viewer. This view shows the correspondences between maps in a rice sequence map set and maps in a rice QTL map set. The number of correspondences between each map is given as the first number, and the number of maps involved is given in parentheses. The second is useful when viewing the matrix at the map set level (not shown). View Image -
Figure 9.8.12 A view of a rice sequence map without using the collapse_features option. Thousands of redundant features are drawn. The actual image continues for eleven more screen widths which makes this view unusable and quite slow to load. View Image -
Figure 9.8.13 The map is using the collapse_features option resulting in a cleaner and quicker view of the map. View Image -
Figure 9.8.14 All of the feature types in this view are set to always display. View Image -
Figure 9.8.15 The feature types in this view are set to only display features with correspondences resulting in a cleaner look. Each feature type default can be set individually. View Image -
Figure 9.8.16 Correspondences can be aggregated into a single line (as shown) or two lines to decrease the number of lines on the screen. View Image -
Figure 9.8.17 The initial CMap menu allows the user to select a species and a map set. View Image -
Figure 9.8.18 After selecting a map set, the user can select from a list of maps in the selected set. The user can also preselect the map start and stop (if selecting a single map) and the feature display options. View Image -
Figure 9.8.19 An initial view of two test maps imported from the tabtest1 file. View Image
Videos
Literature Cited
| Internet Resources | |
| https://sourceforge.net/project/showfiles.php?group_id=27707 | |
| The location of the CMap package. | |
| http://www.gramene.org | |
| The Gramene project Web site for which CMap was initially created. | |
| http://www.gmod.org | |
| The Generic Module Organism Database project Web site. | |
| http://www.gmod.org/cmap | |
| The CMap home page. |
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library
