On representation of proteins by star-like graphs

Similarity analysis for DNA sequences based on chaos game representation. Case study: The albumin

“…In recent years many different graphical representations of DNA/protein sequences have been reported (Gates, 1986;Roy et al, 1998;Li et al, 2006;Randiü et al, 2007;González-Díaza et al, 2009; and the references therein).…”

2-D graphical representation of protein sequences and its application to coronavirus phylogeny

“…Therefore, extension of DNA graphical representations to those of proteins would increase enormously the number of possible alternative assignments for the 20 amino acids making such generalizations unacceptable, which is probably the most important reason why graphical representations of proteins have not been advanced. Recently, however, several schemes have been proposed in the literature which offered some progress for depicting proteins and thus allowing visual inspection of proteins (25)(26)(27)(28)(29). It is interesting that almost all of these representations of proteins are similar to the chaos game representation (CGR) of DNA sequences proposed by (6).…”

“…The graphical representation of proteins was obtained by starting in the center of the circle following amino acid sequence by moving half way towards to corresponding amino acid. In addition, by assigning the 20 amino acids to 20 points on the circumference of a unit circle (29) defined orientations for 20 branches of a star graph. Then they located vertices depicting multiple occurrence of each kind of amino acid on the corresponding branch.…”

Milestones in graphical bioinformatics

“…In such situations, Kowalski and Bender [88] recommended that one rescale the units used to the same numerical interval, such as (21,11). There are three quantities that are combined into our analysis: protein charge (coordinate x), protein mass (coordinate y), and protein abundance (coordinate z).…”