An efficient method for measuring the similarity of protein sequences.
An accurate numerical descriptor for protein sequence is introduced. It is basically a set of each three successive amino acids in the sequence (triplet), starting from left to right, in addition to the distances between each two successive amino acids in the triplet such that the summation of these distances does not exceed 8. This numerical descriptor combines two features the amino acid composition and the position of each amino acid relative to the other nearby amino acids. This numerical descriptor is used to measure the similarity between protein sequences in three sets: NADH dehydrogenase subunit 5 (ND5) proteins of different species, 24 transferrin proteins from vertebrates and 12 proteins of baculoviruses. High correlation coefficient values between our results and the results of ClustalW program are obtained. These values are higher than the values obtained in many other related works.
a Faculty of Science, Department of Biophysics , Cairo University , Giza , Egypt.
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El-Lakkani
a Faculty of Science, Department of Biophysics , Cairo University , Giza , Egypt.
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Lashin
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D016367:Baculoviridae / Q000737:chemistry; D004265:DNA Helicases / Q000737:chemistry; D042967:Electron Transport Complex I / Q000737:chemistry; D006801:Humans; D021122:Protein Subunits / Q000737:chemistry; D020539:Sequence Analysis, Protein / Q000379:methods*; D013045:Species Specificity; D014168:Transferrin / Q000737:chemistry; D014714:Vertebrates; D014764:Viral Proteins / Q000737:chemistry
D000596:Amino Acids; D021122:Protein Subunits; D014168:Transferrin; D014764:Viral Proteins; D004265:DNA Helicases; D042967:Electron Transport Complex I
Similarity analysis; correlation and significance analysis; numerical descriptor; protein sequences