Hierarchy Browser - Help

Help Topics:

:: Taxonomy Choices :: Display Depth :: Selecting Sequences
:: Data Set Options :: Search :: Download
:: Browse :: Viewing Sequences :: Saving/Retrieving Seq cart
:: ARB Import Help :: Start Over

:: 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.

:: Browse

The lineage will display the ancestors of the current root taxon, starting from the highest to the lowest rank. Each taxon is followed by a short description of the status, including the number of selected sequences, total number of sequences assigned to that taxon and the number of search hits 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. Toggle the button before a taxon to open closed or closeclosed the sequences directly assigned to that taxon.

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

If you want to switch to a different taxonomy, see “Start Over” below. 

:: 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.  

:: Search

The Search feature allows you to enter a keyword or keywords for matching against the RDP sequence identifiers and full sequence descriptions.

Our search uses the Lucene search engine developed by the Apache Jakarta project.

Want to narrow or broaden searches? Go back to "Data Set Options" and select a different data set. 

:: Selecting Sequences

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. The number of sequences you have selected under the current data set will be displayed in the status description of the taxons. As you browse, the total number of selections in all data sets is displayed at the top of the page. You can download the selections for local use (see "Download" below). 

:: Viewing Sequences

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

:: Download

The Download page allows you to make choices about the formats of your data and data sets.

Download Formats: Currently three file formats are available for downloading your sequences — GenBank, Fasta and Phylip. The phylip format does not allow "Remove all gaps" and is limited to 2000 sequences.

Alignment Gaps:

Navigation Tree: Download Navigation Tree in newick tree format. It can be imported into ARB. See ARB import help for more details

RNA Distance Matrix: The output format of the matrix is DNADist. If two sequences do not overlap, the output of the distance between these two sequences will be "?". Selecting "Display RDP ID" will display RDP SID (i.e., S000380829) in the output file. Selecting "Display Genbank ACCN" will display Genbank accession and the sequence region (i.e., J01695.1:1518..3059) in the output file.

Data Set Options: Allow you to narrow the dataset from which you want to download. See Data Set Options on the top of this help page. Click the "Refresh" button to update the dataset options.

After choosing the appropriate settings, click on the "Download" button to retrieve your sequences. 

:: Saving/Retrieving Seq Cart

Clicking the seqCART link on the top right of the page will open the Sequence Cart page. Clicking the "Save Cart" button will save the RDP sequence identifier and short description of all the selected sequences (from both the public RDP release and your aligned private myRDP sequences) to a file.

The saved sequences can be retrieved later by using the retrieve function below. If the uploaded cart contains myRDP sequence identifiers, only myRDP sequences for which the researcher has valid access rights, either directly or as a Research Buddy, will be retrieved. You can also upload a file with a list of GenBank accession numbers. Select the correct file content type before you click the "Retrieve Cart" button. If any IDs from the retrieved file cannot be matched to sequences in the current RDP release or your myRDP account, clicking the "View problem IDs" button under the search box in the browser result window will pop-up a new window with a list of the unknown IDs.

The sequence cart can be reset by clicking the "Reset Cart" button.  

:: Start Over

Clicking on the start over link on the right top of the page will take you back to the start page.


Questions/comments: rdpstaff@msu.edu
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