Prediction of nuclear export signals using weighted regular expressions (Wregex)

Motivation: Leucine-rich nuclear export signals (NESs) are short amino acidmotifs that mediate binding of cargo proteins to the nuclear export receptor CRM1, and thus contribute to regulate the localization and function of many cellular proteins. Computational prediction of NES motifs is of great interest, but remains a significant challenge. Results: We have developed a novel approach for amino acid motif searching that can be used for NES prediction. This approach, termed Wregex (weighted regular expression), combines regular expressions with a position-specific scoring matrix (PSSM), and has been implemented in a web-based, freely available, software tool. By making use of a PSSM, Wregex provides a score to prioritize candidates for experimental testing. Key features of Wregex include its flexibility, which makes it useful for searching other types of protein motifs, and its fast execution time, which makes it suitable for large-scale analysis. In comparative tests with previously available prediction tools, Wregex is shown to offer a good rate of true-positive motifs, while keeping a smaller number of potential candidates.