Patterns – Type-In

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 File Explanation.html.

To apply the method:

1. Double click on the method name in the Method Curtain.

2. Type in a Name for the pattern.

3. Type in the Pattern itself in the appropriate fields.
   
   
   • To incorporate inclusive expressions in your pattern, use square brackets around whichever bases are acceptable. Example: “[CG ]” means C or G is acceptable.
     
     
   • For exclusive expressions, use curly brackets around whichever bases are unacceptable. Example: “{AT} ” means neither A nor T is acceptable.
     
     
   • To avoid typing repeated expressions, type the base, followed by the number of repeats in parentheses. Example: “AG(3)T” would search for the string AGGGT;.
     
     
   • For gapped expressions, type in the symbol X followed by the acceptable maximum number of gaps. Example: “AX(1,3)G” would recognize the following sequence strings: AXG, AXXG, AXXXG.

4. Set the Threshold to specify how many mismatches you will permit.
   
   
   • This method will not gap a pattern unless it is part of the syntax.
     
     
   • If you have used ambiguous characters or inclusive expressions, keep the Threshold high to avoid false matches.

To change method parameters:

1. Double click on the method name in the Method Curtain or select the method display

2. Select Analysis > Method Parameters. This returns you to the Type-In Pattern dialog.