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Volume 5

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In Silico Biology 5, 0038 (2005); ©2005, Bioinformation Systems e.V.  

CMDWave: Conserved motifs detection using wavelets

Tariq Riaz, Kuo-Bin Li, Francis Tang and Arun Krishnan*

Bioinformatics Institute 30 Biopolis Street, Singapore 138671, Singapore

* Corresponding author; E-mail:

Edited by E. Wingender; received May 30, 2005; revised June 17, 2005; accepted June 27, 2005; published July 08, 2005


CMDWave (Conserved Motif Detection using WAVElets) is a web server that predicts conserved motifs in protein sequences. A set of query protein sequences are first aligned using ClustalW to obtain equal sized sequences. CMDWave then converts the sequences into a numerical representation using electron-ion interaction potential (EIIP). This is followed by a wavelet decomposition and reconstruction. A new similarity metric along with thresholding is then used to identify conserved motifs across all the query sequences. Users need not specify the number of motifs to be identified. For larger groups of sequences, results can be emailed to the users.


Keywords: motif detection, physicochemical properties, wavelet analysis