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Sequence Result Browser
Results Browser shows the results of searches with sequence queries. On this page you can
- browse search results and all their annotations
- mine the results through filtering, grouping and sorting
- save virtual databases
- export sequences associated with results in standard formats and
- launch applications.
Results Browser shows the results of searches with sequences as queries. It is slightly different from the database browser which shows results from an annotation search (where query is a keyword).
In this results browser page, you can view sequence alignments, annotations of the sequences and you can do various operations on the sequences involved in the alignments.
Overall Page Layout
Most of the results browser page is occupied by a table showing a list alignments returned by your sequence search. The following picture shows the result of searching 21 sequences of human ion channels (from RefSeq) against all of Genbank.
The overall layout above shows the following areas:
- Bread crumb. This area shows how you got here. In this case, you can see the name I gave this result viz. CDR search.
- Filtering. This button opens the filtering widget which can be used to filter out unwanted results.
- Grouping. This button opens the Grouping Widget which allows you to group your results in different ways and to apply filters on groups.
- Top level menu bar explained here
- Pagination. This area allows you to scroll through pages of results (if there are multiple) by using the next, previous, first and last page links.
- Total number of results. This is the area where the total number of results returned is displayed.
- Selection Cart. Displays how many results you have selected through the check-boxes.
Viewing Alignments And Annotations
Browse results in the list by mousing over on to them. When you mouse over to a result, the item is highlighted in yellow.
To view the alignment from the result, click on it when it is highlighted. To close the alignment, either click the Close link at the top right of the annotation window or go back to the highlighted area and click.
An alignment is a pair-wise match between a query and a subject sequence. In the alignment window, you can view other data associated with this alignment by clicking the appropriate tabs.
- Subject Annotation shows annotation of the subject.
- Subject sequence shows the sequence of the subject.
- Query sequence shows the sequence of the query.
Operations On Results
Results browser provides several powerful operations on results for mining them.
- Filtering. To remove any results you don't want from the display, apply a filter. For full details see the filtering widget help page.
The fields on which filters can be applied include alignment parameters (like percent identity of alignment) as well as annotation parameters (like Organism, sequence length) is dependent on the database. All annotation fields in the subject databases are available for filtering.
- Grouping. You can group the results; to see how many organisms are represented in the search, group by organism. For full details see the Grouping Widget help page.
By default, your search results are grouped by query. Therefore, to go back to the default view, click View -> Group by -> Query.
- Sorting. To change the order in which sequences appear, click the header of any column. This sorts the sequences according to contents of that column. For example, to sort all entries by gene name, click on the Gene Name column header.
- Changing the columns displayed. To change the columns displayed follow directions on the Top Level Menu help page for the view menu.
- Selecting Results. To select a result, click the checkbox to its left.
Top Level Menu
The top level menu, provides operations for launching 3rd party applications, exporting sequences, creating reports and creating a virtual database. For full details consult the help page for the top level menu.