A new algorithm is introduced for analyzing gene-duplication-independent (orthologous) and gene-duplication-dependent amino acid sequence similarities between proteins of different species. It is based on the calcn. of an autocorrelation function D(x) as a Fourier series analogous to that used in crystal anal. by x-ray diffraction. The primary structure of the protein is decompd. into homopolypeptide-defective sequences contg. identical or similar amino acid residues and vacancies corresponding to the missing amino acid residues. The Fourier transforms F(h) simulating the diffraction patterns of defective linear gratings corresponding to the defective homopolypeptide sequences are calcd. The squared F(h) values are then used as coeffs. of Fourier series corresponding to the autocorrelation functions D(x). A peak of D(x) corresponds to a vector of length x, which is the distance between 2 identical amino acid residues. Optical diffraction methods, instead of computer methods, would also be useful. It is shown through a no. of examples that this method allows satisfactory pattern recognition of homologies and internal duplications of an initial segment of the polypeptide chain. In the latter case the value of the above method may be seen from the fact that it detects repeated duplications in proteins such as spinach ferredoxin and myoglobin, for which other methods had either failed or given inconclusive results. The above approach appears most promising for studies of mol. evolution and structure-sequence correlations.

Pattern Recognition of Sequence Similiarities in Globular Proteins by Fourier Analysis: A Novel Approach to Molecular Evolution / Liquori, A. M.; Ripamonti, A; Sadun, Claudia; Ottani, S; Braga, D.. - In: JOURNAL OF MOLECULAR EVOLUTION. - ISSN 0022-2844. - STAMPA. - 23:(1986), pp. 80-87. [10.1007/BF02101001]

Pattern Recognition of Sequence Similiarities in Globular Proteins by Fourier Analysis: A Novel Approach to Molecular Evolution

SADUN, Claudia;
1986

Abstract

A new algorithm is introduced for analyzing gene-duplication-independent (orthologous) and gene-duplication-dependent amino acid sequence similarities between proteins of different species. It is based on the calcn. of an autocorrelation function D(x) as a Fourier series analogous to that used in crystal anal. by x-ray diffraction. The primary structure of the protein is decompd. into homopolypeptide-defective sequences contg. identical or similar amino acid residues and vacancies corresponding to the missing amino acid residues. The Fourier transforms F(h) simulating the diffraction patterns of defective linear gratings corresponding to the defective homopolypeptide sequences are calcd. The squared F(h) values are then used as coeffs. of Fourier series corresponding to the autocorrelation functions D(x). A peak of D(x) corresponds to a vector of length x, which is the distance between 2 identical amino acid residues. Optical diffraction methods, instead of computer methods, would also be useful. It is shown through a no. of examples that this method allows satisfactory pattern recognition of homologies and internal duplications of an initial segment of the polypeptide chain. In the latter case the value of the above method may be seen from the fact that it detects repeated duplications in proteins such as spinach ferredoxin and myoglobin, for which other methods had either failed or given inconclusive results. The above approach appears most promising for studies of mol. evolution and structure-sequence correlations.
1986
01 Pubblicazione su rivista::01a Articolo in rivista
Pattern Recognition of Sequence Similiarities in Globular Proteins by Fourier Analysis: A Novel Approach to Molecular Evolution / Liquori, A. M.; Ripamonti, A; Sadun, Claudia; Ottani, S; Braga, D.. - In: JOURNAL OF MOLECULAR EVOLUTION. - ISSN 0022-2844. - STAMPA. - 23:(1986), pp. 80-87. [10.1007/BF02101001]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/88217
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