Welcome to the Wregex (v2.1) home page


We present a novel approach for amino acid motif searching termed Wregex (weighted regular expression), which combines regular expressions with a Position-Specific Scoring Matrix (PSSM).

This website provides the following pages:

Wregex website pages
NameDescription
Home The Wregex home page.
Search Search motifs in protein sequences provided as an input fasta file. The motif can be selected from a dropdown list or a custom motif can be provided by the user by entering a regular expression and an optional PSSM. This PSSM can be built using the Training page.
Charts Browse charts with most interesting Wregex motif candidates.
Training Build a custom PSSM by providing a regular expression and a set of training motifs. Please read first the user manual to get familiar with matching groups in Wregex regular expressions.
Documentation Here there is the user manual and a paper explaining the details of the Wregex algorithm.
Downloads Wregex is free software and licensed under the GPL. In this page you can find a link to the source code and the binary redistributable.

Funding: The maintenance of this website is supported by the Basque Country Government Department of Industry (SAIOTEK S-PE12UN005) and the University of the Basque Country (UFI11/20).

This project has been developed in the context of the EhuBio collaboration. For further information please contact wregex@ehubio.es.

Site last updated: Sep 26, 2017

Latest news


  • Sep 26, 2017 - Wregex v2.1 published
  • Sep 14, 2017 - Updated to latest versions of COSMIC and UniProt
  • May 12, 2016 - Wregex v2.0 published in Scientific Reports
  • Dec 29, 2014 - Finished COSMIC support
  • Apr 16, 2014 - Included time constraints to avoid denial of service to other users
  • Mar 26, 2014 - Included bubble charts
  • Feb 10, 2014 - Included human proteome as a predefined target
  • Jan 06, 2014 - Wregex v1.0 published in Bioinformatics