So to understand protein sequences, we are to first understand structure of amino acids (peptides) given below: As sequences, Protein’s primary structures differ externally due to the number and relative position of the peptides in the chain. The peptides are linked together just as the compartments of a train by what is called a peptide bond. Externally Protein’s primary structures are sequences of 20 peptides (amino acids). In fact, by a protein sequence, we mean primary structure of a protein. To discuss similar aspects in protein sequences, we are to understand what we actually mean by a protein sequence. But there is no method of comparison using directly Bio-chemical properties, because they are not enough for the purpose. Representations based on such classified groups are obtained for Genome sequences and methodologies are developed for their comparisons accordingly. To begin with, it may be mentioned that in case of genome sequences owing to Bio-chemical properties, the nucleotides are classified in the following groups: (R/Y) ,(M/K) and (W/S), where R=(A, G) and Y=(C, T), M=(A, C) and K=(G, T), W=(A, T) and S=(C, G). The purpose of the review is three fold: First to highlight different types of methodologies used so far in connection with protein sequence comparison based on physio-chemical properties of amino acids second to find out if there is any mathematical discrepancies in any one of the methodologies, and if so, to suggest proper way out to make them sound and workable lastly to suggest some novel methods of comparison for protein sequence comparison based on physio-chemical properties of amino acids. It also suggests some possible open problems. Finally it tries to point out how to modify the methods, in case they are not sound. It also tries to examine critically all the methods under mathematical precision. Next it tries to sum up different types of methodologies used so far in protein sequence comparison based on physio-chemical properties of amino acids. The review tries to list out maximum number of physical and chemical properties of amino acids, which are being used directly or indirectly in protein sequence comparison.
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