Protein sequence comparison under a new complex representation of amino acids based on their physio-chemical properties

Abstract

The paper first considers a new complex representation of amino acids of which the real parts and imaginary parts are taken respectively from hydrophilic properties and residue volumes of amino acids. Then it applies complex Fourier transform on the represented sequence of complex numbers to obtain the spectrum in the frequency domain. By using the method of ‘Inter coefficient distances’ on the spectrum obtained, it constructs phylogenetic trees of different Protein sequences. Finally on the basis of such phylogenetic trees pair wise comparison is made for such Protein sequences. The paper also obtains pair wise comparison of the same protein sequences following the same method but based on a known complex representation of amino acids, where the real and imaginary parts refer to hydrophobicity properties and residue volumes of the amino acids respectively. The results of the two methods are now compared with those of the same sequences obtained earlier by other methods. It is found that both the methods are workable, further the new complex representation is better compared to the earlier one. This shows that the hydrophilic property (polarity) is a better choice than hydrophobic property of amino acids especially in protein sequence comparison.

Selection of Moment Vectors in Protein Sequence Comparison Under Binary Representation

“…Volumes and Hydrophilicity & Residue Volume of ND6 protein sequences as found in [34]. It also re ects the exact relationship of the species as obtained by the present method.…”

“…To check the strength of proposed techniques, a comparison is made with the results obtained by other methods as well. For example, gure-6 and gure-7 show the phylogenetic trees of ND4 protein sequence obtained by the use of complex representation of Amino Acids under Hydrophobicity & Residue Volumes and Hydrophilicity & Residue Volume respectively as found in [34].It re ects the exact relationship of the species as obtained by the present method. Again, Figure -8 shows the phylogenetic tree of the 16 ND5 protein sequences based on the PCA-FFT analysis [35].…”

A Critical Mathematical Review on Protein Sequence Comparison Using Physio-Chemical Properties of Amino Acids

“…a. Can the results of [27,28] be developed avoiding complex representations? Are the conclusions same?…”

“…But no protein sequence comparison based on this representation was considered. The complex representation of amino acids based on the properties of hydrophilicity and residue volumes is used [28]. The representation is not the same as the earlier one [27].…”

“…Anyway ICD method for such a transformation is modified accordingly and with suitable descriptor protein sequence comparison is carried out using Euclidean norm as the distance measure. Interestingly, the protein sequences are compared for both types of representations given in [27,28]. It is found that in the later case, the result is better.…”