Email updates

Keep up to date with the latest news and content from Algorithms for Molecular Biology and BioMed Central.

Open Access Highly Accessed Research

Evaluating deterministic motif significance measures in protein databases

Pedro Gabriel Ferreira* and Paulo J Azevedo

Author Affiliations

Department of Informatics, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal

For all author emails, please log on.

Algorithms for Molecular Biology 2007, 2:16  doi:10.1186/1748-7188-2-16

Published: 24 December 2007

Abstract

Background

Assessing the outcome of motif mining algorithms is an essential task, as the number of reported motifs can be very large. Significance measures play a central role in automatically ranking those motifs, and therefore alleviating the analysis work. Spotting the most interesting and relevant motifs is then dependent on the choice of the right measures. The combined use of several measures may provide more robust results. However caution has to be taken in order to avoid spurious evaluations.

Results

From the set of conducted experiments, it was verified that several of the selected significance measures show a very similar behavior in a wide range of situations therefore providing redundant information. Some measures have proved to be more appropriate to rank highly conserved motifs, while others are more appropriate for weakly conserved ones. Support appears as a very important feature to be considered for correct motif ranking. We observed that not all the measures are suitable for situations with poorly balanced class information, like for instance, when positive data is significantly less than negative data. Finally, a visualization scheme was proposed that, when several measures are applied, enables an easy identification of high scoring motifs.

Conclusion

In this work we have surveyed and categorized 14 significance measures for pattern evaluation. Their ability to rank three types of deterministic motifs was evaluated. Measures were applied in different testing conditions, where relations were identified. This study provides some pertinent insights on the choice of the right set of significance measures for the evaluation of deterministic motifs extracted from protein databases.