Welcome to the GenomeQuest Documentation Wiki
The Grouping widget is available at the top of the GenomeQuest page when browsing results of sequence or keyword search. To access it, simply click the Grouping button.
Note that Grouping is computationally very intensive. Therefore the button is deactivated when the number of results being browsed is very large. If you need to group a result set and find the group button disabled, please contact firstname.lastname@example.org to see if there are other options.
The grouping function is useful for getting different cross sections of a result set. Consider an example where a sequence search returned 1000 results. Through grouping, you can determine that these 1000 results
- come from 233 patent documents (group by patent).
- come from 154 patent families (group by patent family).
- have 483 Organisms among them (group by organism)
Basic Operation of Grouping
Each result in a sequence search is a pari-wise list: 1 query and 1 subject sequence. Key word searching results in a simple list.
To group by a given parameter
- Click the Grouping button.
- Select the parameter to group on from the drop-down menu.
- Select the number of items to see per group through the second drop-down menu.
- When grouping by alignment, the only possible option is to see ALL the results.
- Click the Apply button.
- Click the Reset button to return to the default view.
- For sequence searches, the default grouping is by query sequence, showing three results per group.
- For keyword searches the default view is ungrouped.
In the picture below, when the [Apply] button is clicked, GenomeQuest will only group the results by patent number and show one result per patent.
There is an ability to filter out whole groups from display:
- By Group size: specifying how many members must be in the group.
- By Annotation: Specify keywords that must match in the annotation of
- EVERY member of the group
- at least ONE member of the group or
- ALL members of the group.
The group filtering widget within the grouping area is very similar to the overall filtering widget in terms of how to add new filters and how to remove existing filters.
Patent Search Example of Group Filtering
Imagine that you searched patent databases with three different kinds of sequences, say:
- Multiple forward primers,
- Multiple reverse primers and
- Multiple probes.
Now you would like to group the results by patent and see only those patents that have at least 1 of each type of query (probe, forward primer, reverse primer).
To do this, make the identifiers of your query sequences have descriptive tags. For example:
- Forward primers are named FP_1, FP_2, ...
- Reverse Primers are named RP_1, RP_2, ...
- Probes are named PROB_1, PROB_2, ...
Now run your search. When the results come back, group your results by Patent number and then apply the following GROUP Filters:
- Query Identifier - one member matches - FP*
- AND -
- Query Identifier - one member matches - RP*
- AND -
- Query Identifier - one member matches - PROB*
This will display groups containing at least one each from Forward primer, Probe and Reverse primer.