The present paper develops a novel way of reducing a protein sequence of any length to a real symmetric condensed 20 × 20 matrix. This condensed matrix can be nicely applied as a protein sequence descriptor. In f...The present paper develops a novel way of reducing a protein sequence of any length to a real symmetric condensed 20 × 20 matrix. This condensed matrix can be nicely applied as a protein sequence descriptor. In fact, with such a condensed representation, comparison of two protein sequences is reduced to a comparison of two such 20 × 20 matrices. As each square matrix has a unique Alley Index/normalized Alley Index, such index is conveniently used in getting distance matrix to construct Phylogenetic trees of different protein sequences. Finally protein sequence comparison is made based on these Phylogenetic trees. In this paper three types viz., NADH dehydrogenase subunit 3 (ND3), subunit 4 (ND4) and subunit 5 (ND5) of protein sequences of nine species, Human, Gorilla, Common Chimpanzee, Pygmy Chimpanzee, Fin Whale, Blue Whale, Rat, Mouse and Opossum are used for comparison.展开更多
The paper considers Voss type representation of amino acids and uses FFT on the represented binary sequences to get the spectrum in the frequency domain. Based on the analysis of this spectrum by using the method of i...The paper considers Voss type representation of amino acids and uses FFT on the represented binary sequences to get the spectrum in the frequency domain. Based on the analysis of this spectrum by using the method of inter coefficient difference (ICD), it compares protein sequences of ND5 and ND6 category. Results obtained agree with the standard ones. The purpose of the paper is to extend the ICD method of comparison of DNA sequences to comparison of protein sequences. The topic of discussion is to develop a novel method of comparing protein sequences. The main achievements of the work are that the method applied is completely new of its kind, so far as protein sequence comparison is concerned and moreover the results of comparison agree with the previous results obtained by other methods for the same category of protein sequences.展开更多
文摘The present paper develops a novel way of reducing a protein sequence of any length to a real symmetric condensed 20 × 20 matrix. This condensed matrix can be nicely applied as a protein sequence descriptor. In fact, with such a condensed representation, comparison of two protein sequences is reduced to a comparison of two such 20 × 20 matrices. As each square matrix has a unique Alley Index/normalized Alley Index, such index is conveniently used in getting distance matrix to construct Phylogenetic trees of different protein sequences. Finally protein sequence comparison is made based on these Phylogenetic trees. In this paper three types viz., NADH dehydrogenase subunit 3 (ND3), subunit 4 (ND4) and subunit 5 (ND5) of protein sequences of nine species, Human, Gorilla, Common Chimpanzee, Pygmy Chimpanzee, Fin Whale, Blue Whale, Rat, Mouse and Opossum are used for comparison.
文摘The paper considers Voss type representation of amino acids and uses FFT on the represented binary sequences to get the spectrum in the frequency domain. Based on the analysis of this spectrum by using the method of inter coefficient difference (ICD), it compares protein sequences of ND5 and ND6 category. Results obtained agree with the standard ones. The purpose of the paper is to extend the ICD method of comparison of DNA sequences to comparison of protein sequences. The topic of discussion is to develop a novel method of comparing protein sequences. The main achievements of the work are that the method applied is completely new of its kind, so far as protein sequence comparison is concerned and moreover the results of comparison agree with the previous results obtained by other methods for the same category of protein sequences.
