URL: http://athina.biol.uoa.gr/bioinformatics/waveTM/
Proper Citation: waveTM (RRID:SCR_006199)
Description: A web tool for the prediction of transmembrane segments in alpha-helical membrane proteins. A sliding window of 20 residues is used in order to calculate an average residue hydrophobicity profile, using a hydrophobicity scale. Discrete Wavelet Transform is applied on the average residue hydrophobicity signal and the different frequency coefficients produced are adaptively thresholded so that a denoised signal is reconstructed. A dynamic programming algorithm processes the denoised signal to provide the optimal model for the number, the length and the location of membrane-spanning segments. The end points of the predicted segments are extended to include flanking hydrophobic residues. Topology prediction can also be obtained in conjunction with OrienTM (Liakopoulos et al, 2001). Analysis of a non-redundant test set, provides a ~95% per segment accuracy and ~90% per residue accuracy. Now, you can: * Run waveTM on a sequence * Browse the results obtained with the algorithm * View additional material concerning the hydrophobicity scale
Abbreviations: waveTM
Synonyms: waveTM: Wavelet-based transmembrane segment prediction
Resource Type: analysis service resource, data analysis service, service resource, production service resource
Defining Citation: PMID:15107018
Keywords: wavelet, predict, transmembrane segment, alpha-helical membrane protein, protein, protein sequence, discrete wavelet transform, sequence, hydrophobicity scale, hydrophobicity, transmembrane protein, topology, transmembrane
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University of Athens Biophysics and Bioinformatics Laboratory |
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