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Installing and Configuring CMap
Publication Name:
Current Protocols in Bioinformatics
Unit Number:
Unit 9.8
DOI:
10.1002/0471250953.bi0908s17
Online Posting Date:
March, 2007 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
Table of Contents
- Unit Introduction
- 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: Installing CMap
- Commentary
- Bibliography
- Figures
Figures
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Figure 9.8.1CMap 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. -
Figure 9.8.2The 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. -
Figure 9.8.3Chromosome 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. -
Figure 9.8.4The 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. -
Figure 9.8.5The 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. -
Figure 9.8.6Chromosome 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. -
Figure 9.8.7Maps from Figure -
Figure 9.8.8The 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. -
Figure 9.8.9The 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. -
Figure 9.8.10Tab 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. -
Figure 9.8.11The 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). -
Figure 9.8.12A 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. -
Figure 9.8.13The map is using the collapse_features option resulting in a cleaner and quicker view of the map. -
Figure 9.8.14All of the feature types in this view are set to always display. -
Figure 9.8.15The 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. -
Figure 9.8.16Correspondences can be aggregated into a single line (as shown) or two lines to decrease the number of lines on the screen. -
Figure 9.8.17The initial CMap menu allows the user to select a species and a map set. -
Figure 9.8.18After 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. -
Figure 9.8.19An initial view of two test maps imported from the tabtest1 file.
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. | |
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