Gorka edited this page May 16, 2016 · 3 revisions

Introduction

Original article

Prieto G, Fullaondo A, Rodriguez J A: Prediction of nuclear export signals using weighted regular expressions (Wregex). Bioinformatics (2014) 30 (9): 1220-1227.

DOI: 10.1093/bioinformatics/btu016

URL: http://bioinformatics.oxfordjournals.org/content/30/9/1220

Summary

Wregex (weighted regular expression) offers a new approach for amino acid motif searching. Wregex combines a regular expression with an optional Position-Specific Scoring Matrix (PSSM). The regular expression is used to obtain a candidate list matching the desired conditions, and the PSSM is used for computing a score that can be used to select the most promising of those candidates.

Online use

For online use and the user manual, please go to the official Wregex website http://ehubio.ehu.eus/wregex.

Local installation

You can download the compiled wregex.war file and copy/extract it to webapps in your Apache Tomcat 7 home directory, or you can checkout the source code from the SVN repository and compile your customized version.

In any case you probably want to relax the default Wregex limits in WEB-INF/web.xml.

Wregex uses a predefined set of databases which must be present in the system. You can modify (add/delete) these databases by editing the resources/data/databases.xml file.

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