- Communication -

Volume 4

Full article

waveTM: Wavelet-based transmembrane segment prediction

Evanthia E. Pashou, Zoi I. Litou, Theodore D. Liakopoulos and Stavros J. Hamodrakas*

Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
Phone: +30-210-7274 931, Fax: +30-210-7274 742

*  corresponding author
  Email: shamodr@cc.uoa.gr


Edited by E. Wingender; received October 08, 2003; accepted December 31, 2003; published January 05, 2004

Abstract

waveTM is a web tool for the prediction of transmembrane segments in a-helical membrane proteins. Prediction is performed by a dynamic programming algorithm on wavelet-denoised 'hydropathy' signals. Users submit a protein sequence and receive interactively the results. Topology prediction can also be obtained in conjunction with the algorithm OrienTM. A web server that implements the waveTM algorithm is freely available at http://bioinformatics.biol.uoa.gr/waveTM.

Key words: a-helical transmembrane proteins, prediction, discrete wavelet transform, hydropathy signal, denoising, threshold