About T-RFLP Analysis Program (TAP)

  The T-RFLP Analysis Program was designed to facilitate comparative community analysis using terminal restriction fragment length polymorphisms (T-RFLP). The example below demonstrates a simplified run of of TAP. In addition to the demonstration, a description of the functionality of the interface and the format of the resultant data has been included. For more information about the T-RFLP method, please refer to the paper by T.L. Marsh Curr Opin Microbiol 1999 Jun;2(3):323-7.
   TAP: T-RFLP Analysis Program - Example

  TAP was designed to be run as a Java applet directly from its resident web page. Please refer to this page for a description of what is required to run this program. Once the requirements have been met and the program is loaded, the main TAP window will be displayed with the RDP phylogenetic hierarchy loaded (figure 1). A plus to the left of a phylogenetic group name indicates that it contains subgroups. These can be viewed by pressing the plus symbol.

Figure 1: T-RFLP Analysis Program newly loaded.

To add a new T-RFLP digest to the hierarchy, open the Digest menu and select New. After this, a digest input dialog will be displayed (figure 2) in addition to the main window.

Figure 2: Digest window.

Adding a new digest to the main display is accomplished by entering the primer sequence (IUB compatible), selecting the primer type (forward or reverse), setting the primer's properties, selecting one or more enzymes, selecting the digest type, then pressing the Submit button. NOTE: A delay will occur as the program contacts the web server for the digest information. Additional digests can be added by repeating the aforementioned procedure. Once a digest has been added, the organisms which have been primed and cut will appear within the hierarchy (figure 3). For a particular digest of an organism, the name of the enzyme that produced the shortest fragment is displayed as well as the size of that fragment. If NA NA occurs within a digest column, that particular organism was either not primed or not digested. Organisms can be selected and de-selected clicking any of the information provided in its row. Selected organisms are denoted with a black background.

Figure 3: Hierarchy with multiple digests.

Organisms can be displayed in a sorted format (figure 4) by selecting the button above the column which sorting is desired for, opening the Display menu and selecting Sorted. Reordering can be performed by repeating this procedure. The hierarchical display can be redisplayed by selecting the Phylogeny item of the Display menu.

Figure 4: Sorted display.

A search can be performed for a particular string token or fragment size set via the search window (figure 5). This window can be accessed by opening the Search menu and selecting Find. The search is performed upon the column of data that has its header button selected. To search by fragment size, a digest column must be selected and one or more fragment sizes must be entered in the Find what text field with the sizes separated by spaces. Organisms matching the search criteria are selected (or remain selected). By searching all sequences, found organisms will be added to the set of currently selected organisms. When a search on selected sequences is performed, all initially selected organisms which do not meet the search criteria are deselected.

Figure 5: Search window.



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