SeqMatch Help

Help Topics:

:: Taxonomy Choices :: Data Set Options :: Display Depth
:: Summary :: Selecting Matches :: Print Friend Results
:: Input Format :: Viewing Match Sequences :: Start New Match
:: Result Format :: Download Selected Sequences :: Display KNN Matches

 

:: Taxonomy Choices

Select the taxonomy in which sequences will be displayed. This option is available only on the start page.


:: Data Set Options

Selecting different data sets alters the types of sequences available for browsing. You may select one or both options to restrict the kinds of sequences displayed.


:: Display Depth

Controls the number of ranks displayed in the hierarchy. With the default "Auto" setting, the program automatically adjusts the depth to display a reasonable number of lines in the browser. Increase the depth to see more ranks at the same time.  


:: Summary

The summary page shows where a query sequence belongs to agreed by all the match sequences of that query.

The lineage will display the ancestors of the current root taxon, starting from the highest to the lowest rank. Each taxon is followed by the number of query sequences under that taxon.

The hierarchy view displays all the taxon nodes with sequences assigned to them in the hierarchical order, starting from a root taxon. Each line contains the taxon rank, name and the short description of status. The top taxon is the current root taxon. Clicking any other taxon node will make that node display as the root and will update the hierarchy view.

To change to a different data set, see "Data Set Options". After making the appropriate selections, click the Refresh button to update the view.  


:: Selecting Matches

To select or deselect all sequences below a taxon, click select or deselect in front of that taxon. You can also select or deselect one sequence by checking or unchecking the checkbox before a sequence. This icon partial select indicates a subset of the sequences selected below a taxon. Click partial select once to select all sequences. As you browse, the total number of selections in all data sets is displayed at the top of the page. Click the "Save selection and return to summary" button to go back to summary page. The selections will also be saved in Sequence Cart. You can download the selections for local use (see "Download" below).  


:: Print Friend Results

From the summary page, click on "show printer friendly result" link next to the root taxon, all the match results under that root taxon will be displayed. The results for each query sequence are shown in hierarchical order.  


:: Input Format

Currently Fasta, GenBank and EMBL formats are allowed. Both uppercase and lowercase formatting is allowed. The number of query sequences is limited to 2000. If you need more than 2000 sequences classified, please contact rdpstaff@msu.edu.  


:: Viewing Sequences

Individual sequences can be viewed by clicking on the RDP sequence identifier link (i.e., S000002414).  


:: Start New Match

Clicking on new match link on the right top of each page will remove all the selections you made in the previous browsing experience and take you back to the start page.  


:: Result Format

Each match result line contains six elements, from left to right,

 

:: Download Selected Sequences

The selection can be downloaded from the seqCART on the main tool menu.  


:: Display KNN Matches

Controls the number of matches displayed per sequence, also the number used to classify queries by unanimous vote. The maximum value for k is 20.

 

Questions/comments: rdpstaff@msu.edu
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