Protein sequence analysis based on hydropathy profile of amino acids

Abstract

Biology sequence comparison is a fundamental task in computational biology. According to the hydropathy profile of amino acids, a protein sequence is taken as a string with three letters. Three curves of the new protein sequence were defined to describe the protein sequence. A new method to analyze the similarity/dissimilarity of protein sequence was proposed based on the conditional probability of the protein sequence. Finally, the protein sequences of ND6 (NADH dehydrogenase subunit 6) protein of eight species were taken as an example to illustrate the new approach. The results demonstrated that the method is convenient and efficient.

Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids

“…They categorized the 20 amino acids into different types, including as a word with three to five different letters. Their processes not only describe amino acid sequence, but also determine the similarity/dissimilarity of different protein sequences [14,47,[50][51][52][53][54][55][56][57]. However, their methods only consider the physical information of the sequences that are conserved in a particular amino acid sequences.…”

“…But one distinguished limitation on their methods is the limited sample of sequences which can only determine a fraction of total sequences. Further, few group works with the converted amino acid sequences of proteins into three letter sequence based on the hydropathy profile of amino acid and algor a conditional probability as a new invariant for the protein sequences [14]. Their method can also show the distribution of amino acids at different positions in the sequences.…”

“…Several groups have worked with reduced amino acid alphabets to tackle to the above stated problems by reducing the sample size which can perform at the same level as the full alphabets in correct pair wise alignment of sequences with regards to structure similarity but low sequence identity [12,13]. Recently XIE et al [14] proposed a new method by using hydropathy group of amino acids to analyze the similarity/ dissimilarity of protein sequence based on the conditional probability of the protein sequence [14]. Studies are also done on using the substitution matrices from several protein blocks of aligned sequence segments resulting the characterization of related proteins [15].…”

DV-Curve Representation of Protein Sequences and Its Application

“…The first visualization protein model was proposed by Randić et al until 2004 [19]. Some researchers have studied on graphical representation of protein sequences from different perspectives [20][21][22][23][24][25][26][27][28][29].…”

Rational design of peptide vaccines against the Zika virus through sequence descriptors: Techniques and Problems

“…While Nandy [8][9][10], Nandy and Nandy [11] and Larionov et al [12] have used 2D graphical systems to determine DNA systematics, Liao et al [13,14] used the novel techniques for alignment-free phylogeny to determine sequence ancestry, Wiesner and Wiesnerova [15] found the new methodology giving better insights into germ-plasm identifiers, Gonzalez-Diaz and his group presented several papers using the concept for alignment-free prediction of polygalacturonases [16], alternative "in silico" technique for chemical research in toxicology [17] and predicting antimicrobial drugs and targets [18], Nandy et al [19] were able to model influenza hemagglutinin and neuraminidase interdependence which provided predictability to new possible viral assortments [20]. The technique of numerical characterization was extended to proteins initially by Randic et al [21] and led to several approaches being proposed [6,22,23], analyzing phylogenetic relationships between protein families [24], hydropathy profiles of amino acids [25] and others. Thus, numerical characterization of bio-molecular sequences can be considered to have wide-ranging applicability leading to acceptable results, and occasionally new insights.…”