Patterns – Signal

This method, located in the More Methods section, finds transcription factor binding sites using species-specific sequence patterns. To enable you to search your sequence for known transcription factor binding sites, the TFD.dat file is provided. The data in this file is summarized in the file explanation.html.

The following video shows the method in action.

To apply the method:

1. Double-click on the method name in the Method Curtain to open the Transcription Factor dialog.

2. Locate the appropriate transcription factor file and highlight it.

3. Click Open.

This method does not have any parameters that can be adjusted.

To view the sequence pattern for a particular binding site:

Hold the mouse pointer down on one of the sites displayed on the Assay Document; in a second or two, a text box displays the name of the site, the sequence that was matched, the sequence coordinates, and whether the match to the site is on the top or bottom strand.

To search for one specific transcription factor binding site:

Type in the sequence pattern for the site using the Patterns – Type-in method.

To create your own database of transcription factor binding (or other) sites:

Create a fixed-width text file with the following format and content:

For example, one row in the in the fixed-width text file, would appear as:

The “width” is the field width in characters. The text string for the field should be a maximum of one character fewer than the width, and the last character must be a space. Where text strings are shorter than (width – 1), fill in the fixed-width field with spaces.

Look up information about the Transcription Factors Database:

Use Sites & Features > Look Up Site. The command is only enabled after you add the Patterns – Signal method to the curtain, then apply the method to the sequence. The sub-menu item Description looks up the site information on the Ghosh database, hosted on the DNASTAR website. The sub-menu choice Abstract calls up the reference abstract at NCBI for the paper in which the transcription factor was published. Both choices open a web browser, and multiple selections will open multiple browser windows.