PMID: 11932490Apr 5, 2002Paper

Protein sequence comparison based on the wavelet transform approach

Protein Engineering
Chafia Hejase de TradI Cosic

Abstract

A protein's chemical properties, the chain conformation, the function of the protein and its species specificity are determined by the information contained in the amino acid sequence. Proteins of similar functions have at some level sequential identical amino acid sequences. The closer the phylogenetic relationship, the more similar are the sequences. To find the similarities between two or more protein sequences is of great importance for protein sequence analysis. The differences in the amino acid sequences permit the construction of a family tree of evolution. In this work, a comparison method was devised that is capable of analysing a protein sequence 'hierarchically', i.e. it can examine a protein sequence at different spatial resolutions. Based on a wavelet decomposition of protein sequences and a cross-correlation study, a sequence-scale similarity concept is proposed for generating a similarity vector, which renders the comparison of two sequences feasible at different spatial resolutions (scales). This new similarity concept is an expansion of the conventional sequence similarity, which only takes into account the local pairwise amino acid match and ignores the information contained in coarser spatial resolutions.

References

Mar 1, 1991·Journal of Molecular Recognition : JMR·I Cosic, M T Hearn
Dec 30, 1987·European Journal of Biochemistry·I Cosić, D Nesic
Apr 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·W R Pearson, D J Lipman
Dec 1, 1995·Protein Engineering·V GoffinN L Summers
Mar 1, 1995·Bio/technology·I Cosic

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Citations

May 17, 2006·The Protein Journal·Lin JiangYuanbo Diao
Feb 12, 2010·Medical & Biological Engineering & Computing·E PirogovaI Cosic
Jul 20, 2010·Interdisciplinary Sciences, Computational Life Sciences·Juan LiuWen Zhang
Jan 25, 2007·Journal of Bioinformatics and Computational Biology·Gek-Huey ChuaMasaru Tomita
Jul 13, 2011·Advances in Bioinformatics·Rhydon JacksonPhillip Pfeiffer
Apr 27, 2005·BMC Bioinformatics·Kshitiz GuptaS Ramakumar
Oct 3, 2007·Nonlinear Biomedical Physics·Irena Cosic, Elena Pirogova
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Lina YangHuiwu Luo
Jul 20, 2007·Proteomics·Matthew N DaviesDarren R Flower
Jan 11, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Tao MengPuneeth Iyengar
Jan 9, 2009·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·E PirogovaI Cosic
Jun 30, 2006·IEEE Transactions on Nanobioscience·Tuan D Pham
Sep 10, 2008·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Tuan D PhamStephen T C Wong
Jun 28, 2005·Computational Biology and Chemistry·Zhi-ning WenYi Yang
Mar 23, 2004·Journal of Chemical Information and Computer Sciences·Jianding QiuJinyuan Mo

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