“…We can calculate Topological Indices (TIs) for all these classes of networks representations in order to make a numerical description of DNA and protein sequences (González-Díaz et al, 2008). These descriptors (also known as connectivity indices) allow establishing a relation between the biological properties in small and large molecules (QSAR/QSPR), like proteins and genes, and their molecular structure; without to rely upon sequence alignment (Caballero et al, 2007;Cai and Chou, 2005;Cruz-Monteagudo et al, 2007;Chou and Cai, 2003;Chou and Cai, 2005;Chou and Shen, 2008a;Estrada et al, 2006;Estrada et al, 2002;Fernandez et al, 2007a;Fernandez et al, 2007b;González-Díaz et al, 2007a;González-Díaz et al, 2007b;González-Díaz and Uriarte, 2005;Hall et al, 2003;Molina et al, 2004;Prado-Prado et al, 2007;Vilar et al, 2006;Xiao et al, 2009a). Therefore, these methodologies could be an alternative to sequence alignment for the study of proteins and genes (Durand et al, A c c e p t e d m a n u s c r i p t 5 1997; Hansen et al, 1996;Hofacker et al, 2002;Lecompte et al, 2001;Persson, 2000;Standley et al, 2001;Zhang and Madden, 1997).…”