How to Search

Searching for features is done with a loaded map(s) and on the VCMap database. If you need to load a map, consult the Load a Map page for help on doing this.

How to Search

Begin by selecting "Search -> Find..." from the menu bar or by pressing "CTRL + F" on the keyboard.

A "Find" dialog box will open up. Now you have two options to search by:

Search by Name
Search by Loacation
Advanced Search

Depending on which way you want to search, follow the appropriate instructions below.

VCMap Advanced Search

When the search dialog first appears your view should be what is shown below.

Choose a type of filter using the left drop down menu. Depending on your selection a different type of search method will be added on the right side. This is indicated in selection B in the image below.

To add a search filter click the "+" button shown in selection B in the figure below. This button may be disabled if there are empty search filters.

To remove a search filter click its "-" button on the left hand side. This is shown in selection A in the figure below.

The "Match Any" and "Match All" radio buttons, shown in selection C below allow you to either return results that match all of the search criteria, or to return results matching any of the search criteria.

The database, all loaded maps, and thier hidden annotation will be searched.

The results of the search will be listed. The order of the listing can be changed by clicking on the column names (Name, Type, Start, Stop, Chromosome, Map, Loaded).

Results are marked in the "Loaded" column with "Yes", "No", or "Yes (Hidden)". This column indicates if results have been already loaded into VCMap. Results that have already been loaded are also bolded if they are visible and greyed out if they are hidden.

The number of results returned from the loaded maps and the database will both be under the search bar. You can click on the different results and the corresponding feature will be selected on the map.

Double clicking on features from the database will bring up a dialog giving you the option to load the map associated with that result. A checkbox on the dialog enables you to load the map associated with the result as a backbone map. Double clicking results that are hidden features on the map will bring up a dialog box allowing you to show that specific annotation. An image of the dialog box is shown below.

Notes:

"Feature Name" search terms are NOT case sensitive and they can be found at any point within the name.
e.g. a search for "abc" will match the following:
- ABC
- abc
- 123Abc
- abc123
- 123abcxyz

For the "Location Search" filter, only features that fall completely within the start/stop range on the specified chromosome will be found. The following example will explain what this means:

Name	Start	Stop
A	5	15
B	17	25
C	13	19

A search is performed with the start and stop positions being 10 and 20 respectively. C will be returned because its start and stop positions are both between 10 and 20. Features A and B will not be returned. While A's stop and B's start positions do fall between the searched values, A's start and B's stop positions do not and therefore these features will not be included in the results of the search.

The "Location Search" filter supports the standard genomic coordinate notation used by UCSC. To search a whole chromosome simply use chrXX, chrXX: or chrXX:1-, where chrXX is the chromosome you wish to search. To search from a specified start location to the end of the chromosome type chrXX:start or chrXX:start-, where chrXX is the chromosome you wish to search and start is the starting location of the search. Finally to search from a specific starting and stoping range type chrXX:start-stop, where chrXX is the chromosome you wish to search, start is the starting location of the search, and stop is the ending location of the search. An example search is shown below.

To limit memory usage a maximum of 225,000 results will be loaded from the database.

The "Gene Name" and "Location" filters work the same as the individual "Name Search" and "Location Search" tabs.

The add filter button will disable itself to prevent the addition of un-nessary addition of a search filter (i.e. there is already an empty search filter). The button will re-enable itself Once there are no empty filters.

Generic searches may take longer due to the large number of search results being returned. Sorting operations with large result sets may also take more time.

Additional Information

To view the details of a "loaded" feature the search dialog must first be closed by clicking "Close" (search results will be cleared but the selected feature(s) will stay selected). Once the dialog is closed, you can now view the details. Instructions as to how can be found on the view details page.

A non backbone map will contain only segments of the chromosome. Only the loaded segments will be returned as "loaded" results searched.