Motif search from the Toolbox

The dynamic motifs provide a quick way of routinely scanning a sequence for commonly used motifs, but in some cases a more systematic approach is needed. The motif search in the Toolbox provides an option to search for motifs with a user-specified similarity to the target sequence, and furthermore the motifs found can be displayed in an overview table. This is particularly useful when searching for motifs on many sequences.

To start the Toolbox motif search, go to:

        Toolbox | General Sequence Analysis (Image generalsequenceanalyses)| Motif Search (Image patternsearch)

A dialog window will be launched. Use the arrows to add or remove sequences or sequence lists between the Navigation Area and the selected elements.

You can perform the analysis on several DNA or several protein sequences at a time. In this case, the method will search for patterns in the sequences and create an overview table of the motifs found in all sequences.

Click Next to adjust parameters (see figure 15.30).

Image patternSearchStep2
Figure 15.30: Setting parameters for the motif search.

The options for the motif search are:

Click Next to adjust how to handle the results and then click Finish. There are two types of results that can be produced:

Image patternSearchOutput
Figure 15.31: Sequence view displaying the pattern found. The search string was 'tataaa'.