SynaTate is designed to identify structural and functional motifs in query sequences using the predictability of SynaBASE patterns.

This walkthrough provides a basic guide on how to use SynaTate. It consists of a series of screenshots showing an example of how best to use SynaTate to optimise your research activities.

Note that Test Sequence is a link that provides sample test sequences as queries for all SynaSuite applications.

SynaTate Query/Input screen



Step 1: Specify a query type


Select the query type. In this case, a nucleotide-protein query is selected.

Step 2: Submit query sequence

Next, submit a query sequence. There are three ways to submit the sequence:

(i) Select a sequence from a sequence database / Sequence expression



Select a SynaBASE.



Enter the sequence expression.
Search for a sequence by typing a Keyword or sequence header expression that will pull out the reference sequence(s).


Mouse over the sequence to highlight it. Right click and paste the sequence into the "Sequence Expression" field.

(ii) Query sequence


Select a sequence from "Get test sequence" or key in the sequence in the query sequence field.


When using the "Get test sequence" function, select the sequence of interest by clicking on the "Copy" button beside the sequence. This copies the sequence (valid formats - FASTA or raw format) onto the query sequence field of the input page.


The selected sequence copied onto the query sequence text field.

(iii) Upload query file
Upload a sequence (in FASTA or raw format) contained in a file from your computer.



Step 3: Select Target SynaBASE

Each SynaBASE will have its own set of default parameters/options.



Step 4: Annotate

Click on "Submit Query" to execute SynaTate.



Step 5: SynaTate results page

The first output interface is a dynamic graph that displays the conserved sequence motifs along the sequence length from the analysis of patterns. The plot is displayed in terms of Significance along a query sequence length.

Point the cursor at one of the graphs. Scroll up to zoom in on the graphs. Alternatively, press a hot key on the keyboard by pressing the up arrow key to zoom in or down arrow key to zoom out.

Drag on the scroll bar at the bottom of the graph to view the section of interest.



The functions of each button is as follows:

Refresh Button
To reset the graph to the original view i.e. the first input page.

Show Relative Frequency
To show the Relative Frequency on the graph. It is always drawn by a blue line. To hide the Relative Frequency graph line, simply click on the button again.

Show or Hide SIGNIFICANCE
To show or hide the SIGNIFICANCE graph data.

Show or Hide Keywords bar
The green colored line under the x-axis scale of the graph represents the Keyword associates. Click to hide or show the Keywords line.

Print
To print the graph that is being viewed.

Mouse Control Guide
Provides more features on how to use the graph.





At the MML Legend bar on top of the graph, click on the number in the coloured boxes to highlight the SIGNIFICANCE of that particular MML.
For example, clicking on will highlight the SIGNIFICANCE of the MML8 in the graph. If the Relative Frequency is enabled, then the Relative Frequency for the MML8 will be displayed. Note that only one Relative Frequency is displayed at any one time.

Step 6: View GFF(General Feature Format) text output

To view the GFF text output in the terms of Significance or Relative Frequency, click on the blue colour link on the bottom of the page.



GFF text output in the term of Significance


GFF text output in the term of Relative Frequency


Step 7: Select region

To select a region, left click on the graph, drag the cursor to the desired position and release.

A dotted line will be displayed on the graph indicating the selected region.

Move the cursor over the region again to view the tool tip text indicating the exact position in the region.



Left click on the region to view the selected number of base sequences in the SynaTate Keywords results page. The selected region (user selection) appears centred regardless of the number of bases selected (except if no bases are selected).

SynaTate Keywords results page


All the related Keywords items in the range will be highlighted in the results page. Each of the Keywords items has a different name which is displayed on the right side of each Keywords block. The SynaTate Keywords graph is plotted in terms of Significance.



Left click and drag the cursor to the desired position on the graph to highlight the dotted line boundaries on the selected region. Mouse over the graph to view the position of the region.

View pop-up menu



Right click on the selected region to view the pop-up the menu. There are two options: SynaSearch sequence and Copy sequence.

Note that the SynaSearch sequence and Copy sequence buttons on the right side panel are active after a region has been selected. The functions are identical to the features in the pop-up menu.

SynaSearch sequence
Copy and paste the selected sequence to the text sequence in the SynaSearch input page.



Copy sequence
Copy the sequence on the clipboard.



Print
Directs the user to another printable page. This enables users to print the results conveniently.

Mouse Control Guide
Displays the mouse control guide menu. It guides and directs users on how to perform certain functions on the results.



Reselect region

Return to the first SynaTate output page again; assume that region between 400 and 775 in the first reverse reading frame has been selected. Left click on the region to link to the SynaTate Keywords results page.



In the SynaTate Keywords results, the amino acid sequence is always displayed in a forward direction. Since the selected region is in the reverse frame, the nucleotide sequence and coordination are reversed. Therefore the graph image and Keywords blocks are also reversed.



For more questions and reference guide please contact: support@mgrc.com.my