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Taxomatic Help

This tool displays a color heat map representation of a symmetric distance matrix between large sets of sequences chosen by the user. Close and distant relationships are displayed in contrasting colors. This display makes it easy to visualize errors in an underlying taxonomy. Taxa that are phylogenetically incoherent or are misplaced in a hierarchy stand out visually in the representation, as do individual misplaced sequences.

Sequences can be selected from the RDP database, from myRDP OR an aligned fasta file, or a pre-calculated distance matrix file uploaded by the user. The heat map displays sequences arranged in a predefined taxonomic order. For RDP and myRDP sequences, either the RDP taxonomy or an uploaded user-defined taxonomy can be visualized. Researchers can use pan and zoom features similar to those on Google Maps to examine specific regions of the heat map. Bounding boxes for each taxon are displayed on mouse-over and the corresponding portions of the taxonomic hierarchy are highlighted. At higher zoom levels, sequence and organism specific information are rendered upon mouse-over in the tooltips display.

To accommodate visually impaired users the colors in the heat map display can be selected from a drop-down menu. heat map images, the underlying distance matrix, and the taxonomy are also available for download.

Note: If you are using a small number of sequences (6 or less), try a higher zoom to get the heat map images to render correctly.

Sample Taxomatic Workflow (or How to Use Taxomatic):

browser selection
  1. To begin we'll select a group of type sequences from the hierarchy browser (be sure to change the "Strain" option from "Both" to "Type"). Next we'll select sequences from the orders Rhodobacterales, Hydrogenophilales, and Rhodocyclales.

  2. Select the "Taxomatic" tool from the toolbar.

  3. On the main Taxomatic page you are presented with several options on how to proceed; for the sample we will leave the settings at their defaults and click the "Go" button. For more information on the available options there is a detailed description for each at the bottom of the page.

  1. The Taxomatic interface provides flexibility in how you interact with the heat map. You can pan around the heat map (similar to the Google Maps interface) and zoom in and out. (Note: Once you zoom past 4x, detailed sequence information will be available).

  2. heat map

  1. In this heat map we can see a misplaced group (the genus Shinella should be classified in the family Rhodobacteraceae instead of the family Rhodocyclaceae).

    We can see this because of the band of bright teal (representing large evolutionary distances) around Shinella and the band of yellow (representing small evolutionary distances).

  2. To get more information we can zoom down (typically 8x provides the best trade off of detail and field of view) and search for the sequence S000528093 by typing the ID into the search box above the heat map. When we click "find" the view will recenter on the sequence and we are presented with detailed information about the sequence.

    Below the heat map the name, description, and identifiers associated with the sequence are displayed. On the heat map a tooltip is displayed containing the species name (with the year it was validly published) and any synonyms, the strain identifier the sequence was deposited under, and the genbank accession number for the sequence.

 


 

FAQs - Known Issues with myRDP

bullet  How does Taxomatic pick the default zoom level?

Taxomatic finds the zoom level where the entire heat map can be displayed or 8x (whichever is smaller).

bullet  I cannot see sequence overlays.

Sequence information/overlays are not displayed unless you zoom to 8x or higher.

bullet  I can see tooltips for some sequences but not for others, why is that?

Currently sequence information is only available for sequences that have been catalogued by the Names for Life project.

bullet  The image looks great! Now how can I save it?

Along the bottom of the image there are three links. Click the one labeled "Saveable image" and you will be prompted on where to save the image on your computer. You will get the entire heat map at the current zoom without overlays.

bullet  I want to save the taxonomy information used to create this heat map, how do I do that?

Along the bottom of the image there is a link labeled "Taxonomy"; click it and you will be prompted as to where to save the taxonomy xml file.

bullet  How can I get the distance matrix used to generate this heat map?

Along the bottom of the image there is a link labeled "Distance Matrix"; click this link and you will be prompted as to where to save the distance matrix (in DNADist format).

bullet  What information can I see about any given sequence?

You can see the name of the sequence, the description of the sequence and the RDP Sequence ID/Genbank accession of the sequence just below the heat map if your mouse is over a sequence on the diagonal. If your mouse is over a square off the diagonal then you see information for the sequences that intersect at that point.

bullet  Yellow and Teal may be your favorite color, but what if I want different colors?

You can choose from 6 color pairs. The first color is used to show close sequences, while the second color is for distant sequences.

bullet  I want to find a specific sequence in the heat map, how can I do that?

When you're zoomed in to 8x or more a search box appears above the heat map. Type the sequence identifier (typically the RDP Sequence id) into the box and click "find" and the heat map will recenter and highlight the sequence.

Known Issues with Taxomatic

Note: If you are using a small number of sequences (6 or less), try a higher zoom to get the heat map iamges to render correctly.

 

Questions/comments: rdpstaff@msu.edu
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