Similarity/Dissimilarity Analysis of Protein Sequences Based on a New Spectrum-Like Graphical Representation

Abstract

Sequence comparison is one of the foundations in bioinformatics, which can be used to study evolutionary relations among the sequences. In this study, a 2D spectrum-like graphical representation of protein sequences is presented based on the hydrophobicity scale of amino acids. The frequencies of amplitudes of 4-subsequences are adopted to characterize a spectrum-like graph, and a 17D vector is used as the descriptor of protein sequence. The χ2 value of compatibility test is performed. New similarity analysis approach is illustrated on the all protein sequences, which are encoded by the mitochondrion genome of 20 different species. Finally, comparison with the ClustalW method shows the utility of our method.

Research Article The use of bioinformatics tools to characterize a hypothetical protein from <i>Penicillium</i> <i>rubens</i>

“…This is one of the most used and reliable tools on searching for sequence similarity and identity. Sequence similarity comparison, such as for DNA, RNA, and protein, is the base of bioinformatics, and this kind of analysis improve the protein function prediction, being one of the most important analysis in HPs characterization (Pearson, 2013;Yao et al, 2014).…”

An alignment-free method for bulk comparison of protein sequences from different species

“…On the other hand, ClustalW also correctly separates the proteins into their correct groups (Fig.7). Yao et al [18] Ellakani and Mahran [27] Zhang et al [15] Mu et al [28] Liu et al [29] Wu et al […”

“…Authors showed that the proposed model is easier and quicker in handling protein sequences than multiple alignment methods and gives protein classification greater evolutionary significance at the amino acid sequence level. In [18], author presented a 2D spectrumlike graphical representation of protein sequences based on the hydrophobicity scale of amino acids. The frequencies of amplitudes of 4-subsequences were adopted to characterize a spectrum-like graph, and a 17D vector was used for numerical representation of a protein sequence.…”

One novel representation of DNA sequence based on the global and local position information

“…For the widespread application of the moment of inertia in many gene numerical representation method 10 , 11 , 15 , 16 , the normalized moments of inertia for each massive sub-curve of Fermat spiral are calculated as the numerical representation of formal DNA sequence in this paper. To the convenience of calculation, the transformation of polar coordinates to plane coordinates is performed: …”