To evaluate the accuracy of a motif search program is necessary to compare the predictions that this program produces in a set of annotated sequences with the real coordinates of the motifs on such sequences.

For instance, the real motifs here are located in a real promoter sequence:


And these could be the predictions of a pattern discovery program:


You can see that:
- The predicted motif1 is perfectly supported by a real annotation
- The predicted motif2 is partially supported by a real annotation
- The third real site is not detected in the predictions
- The predicted motif3 is not supported by any real data


Graphically, the comparison is easier:



In the output of the Evaluator program, a set of typical accuracy measures are displayed. Essentially, these values are useful to measure the sensitivity to capture the real sites and the specificity to avoid artifacts in the predictions.



A complete summary of the accuracy values is included within the output.
For further information, check the following references:

- Burset, M. and Guigo, R. Evaluation of gene structure prediction programs. Genomics 34: 353-367 (1996).

- Tompa et al. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 23: 137-144 (2005).

• To explore the ABS database follow this link



• To evaluate the predicted motifs in a set of sequences using a reference set of annotated sites follow this link