A new graphical representation of similarity/dissimilarity studies of protein sequences

References

• Randic , M , Novic , M , Vikic-Topic , D and Plavsic , D . 2006 . Novel numerical and graphical representation of DNA sequences and proteins . SAR QSAR Environ. Res. , 17 : 583 – 595 .
   PubMed Web of Science ®Google Scholar
• Gates , MA . 1986 . A simple way to look at DNA . Theor. Biol. Med. Model. , 119 : 319 – 328 .
   Web of Science ®Google Scholar
• Randic , M , Novic , M , Nandy , A and Basak , SC . 2000 . On 3D graphical representation of DNA primary sequences and their numerical characterization . J. Chem. Inf. Comput. Sci. , 40 : 1235 – 1244 .
   PubMedGoogle Scholar
• Zhang , CT and Zhang , R . 1991 . Analysis of distribution of bases in the coding sequences by a diagrammatic technique . Nucleic Acids Res. , 19 : 6313 – 6317 .
   PubMed Web of Science ®Google Scholar
• Randic , M , Novic , M , Lers , N and Plavsic , D . 2003 . Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation . Chem. Phys. Lett. , 371 : 202 – 207 .
   Web of Science ®Google Scholar
• Yau , SS-T , Wang , J , Niknejad , A , Lu , C , Jin , N and Ho , YK . 2003 . DNA sequence representation without degeneracy . Nucleic Acids Res. , 31 : 3078 – 3080 .
   PubMed Web of Science ®Google Scholar
• Yao , YH , Dai , Q , Nan , XY , He , PA , Nie , ZM , Zhou , SP and Zhang , YZ . 2008 . Analysis of similarity/dissimilarity of DNA sequences based on a class of 2D graphical representation . J. Comput. Chem. , 29 : 1632 – 1639 .
   PubMed Web of Science ®Google Scholar
• Yao , YH , Nan , XY and Wang , TM . 2006 . A new 2D graphical representation: Classification curve and the analysis of similarity/dissimilarity of DNA sequences . J. Mol. Struct.-Theochem. , 764 : 101 – 108 .
   Web of Science ®Google Scholar
• Jeffrey , HI . 1990 . Chaos game representation of gene structure . Nucleic Acids Res. , 18 : 2163
   PubMed Web of Science ®Google Scholar
• Stuart , GW , Moffett , K and Baker , S . 2002 . Integrated gene and species phylogenies from unaligned whole genome protein sequences . Bioinformatics , 18 : 100 – 108 .
   PubMed Web of Science ®Google Scholar
• Qi , J , Wang , B and Hao , BL . 2004 . Whole genome prokaryote phylogeny without sequence alignment: A K-string composition approach . J. Mol. Evol. , 58 : 1 – 11 .
   PubMed Web of Science ®Google Scholar
• Yu , ZG , Anh , V and Lau , KS . 2004 . Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses . J. Theor. Biol. , 226 : 341 – 348 .
   PubMed Web of Science ®Google Scholar
• Randic , M . 2004 . 2-D graphical representation of proteins based on virtual genetic code . SAR QSAR Environ. Res. , 15 : 147 – 157 .
   PubMed Web of Science ®Google Scholar
• Randic , M , Zupan , J and Balaban , AT . 2004 . Unique graphical representation of protein sequences based on nucleotide triplet codons . Chem. Phys. Lett. , 397 : 247 – 252 .
   Web of Science ®Google Scholar
• Randic , M , Mehulic , K , Vukicevic , D , Pisanski , T , Topic , DV and Plavsic , D . 2009 . Graphical representation of proteins as four-color maps and their numerical characterization . J. Mol. Graph. Model. , 27 : 637 – 641 .
   PubMed Web of Science ®Google Scholar
• Bai , FL and Wang , TM . 2006 . On graphical and numerical representation of protein sequences . J. Biomol. Struct. Dyn. , 23 : 537 – 545 .
   PubMed Web of Science ®Google Scholar
• Randic , M , Novic , M and Vracko , M . 2008 . On novel representation of proteins based on amino acid adjacency matrix . SAR QSAR Environ. Res. , 19 : 339 – 349 .
   PubMed Web of Science ®Google Scholar
• Randic , M . 2007 . 2-D Graphical representation of proteins based on physicochemical properties of amino acids . Chem. Phys. Lett. , 440 : 291 – 295 .
   Web of Science ®Google Scholar
• Yao , YH , Dai , Q , Li , C , Nan , XY , He , PA and Zhang , YZ . 2008 . Analysis of similarity/dissimilarity of protein sequences . Proteins , 73 : 864 – 871 .
   PubMed Web of Science ®Google Scholar
• Yao , YH , Dai , Q , Li , L , Nan , XY , He , PA and Zhang , YZ . 2010 . Similarity/dissimilarity studies of protein sequences based on a new 2-D graphical representation . J. Comput. Chem. , 31 : 1045 – 1052 .
   PubMed Web of Science ®Google Scholar
• Wen , J and Zhang , YY . 2009 . A 2D graphical representation of protein sequence and its numerical characterization . Chem. Phys. Lett. , 476 : 281 – 286 .
   Web of Science ®Google Scholar
• Li , C , Yu , XQ , Yang , L , Zheng , XQ and Wang , ZF . 2009 . 3-D maps and coupling numbers for protein sequences . Physica A , 388 : 1967 – 1972 .
   Web of Science ®Google Scholar
• Randic , M , Butina , D and Zupan , J . 2006 . Novel 2-D graphical representation of proteins . Chem. Phys. Lett. , 419 : 528 – 532 .
   Web of Science ®Google Scholar
• Randic , M , Zupan , J and Vikic-Topic , D . 2007 . On representation of proteins by star-like graphs . J. Mol. Graph. Model. , 26 : 290 – 305 .
   PubMed Web of Science ®Google Scholar
• Tuller , T , Chor , B and Nelson , N . 2007 . Forbidden penta-peptides . Protein Sci. , 16 : 2251 – 2259 .
   PubMed Web of Science ®Google Scholar
• Bresell , A and Persson , B . 2007 . Characterization of oligopeptide patterns in large protein sets . BMC Genomics , 8 : 346
   PubMed Web of Science ®Google Scholar