Event submissions
EventsMOL2NET'15, Conference on Molecular, Biomed., Comput. & Network Science and Engineering, 1st ed.
Published
This submission belongs to the session 01. CHEMBIO.INFO-01: Cheminfo., Chemom., Comput. Quantum Chem. & Bioinfo. Congress, Cambridge, UK-Chapel Hill and Richmond, USA, 2015 of the event MOL2NET'15, Conference on Molecular, Biomed., Comput. & Network Science and Engineering, 1st ed.
Published date
04 Dec, 2015
Citation
Reinaldo Molina Ruiz, Agostinho Antunes, Guillermin Agüero-Chapin, TI2BioP: Topological Indices to BioPolymers, in Proceedings of MOL2NET'15, Conference on Molecular, Biomed., Comput. & Network Science and Engineering, 1st ed., 5 December–15 December 2015, MDPI: Basel, Switzerland, doi: 10.3390/MOL2NET-1-F011
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TI2BioP: Topological Indices to BioPolymers
Guillermin Agüero-Chapin 1,2
Reinaldo Molina Ruiz 3
Agostinho Antunes 2,4
1. CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n 4450-208 Matosinhos, Porto, Portugal.
2. Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
3. Centro de Bioactivos Químicos, Universidad Central “Marta Abreu” de Las Villas (UCLV), Santa Clara, 54830, Cuba
4. CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal
Abstract
TI2BioP (Topological Indices to BioPolymers) is a software to estimate topological indices (TIs) from two-dimensional (2D) graphical approaches for the natural biopolymers DNA, RNA and proteins The methodology mainly turns long biopolymeric sequences into 2D artificial graphs such as Cartesian and four-color maps but also reads other 2D graphs from the thermodynamic folding of DNA/RNA strings inferred from other programs. The topology of such 2D graphs is either encoded by node or adjacency matrixes for the calculation of the spectral moments as TIs. These numerical indices were used to build up alignment-free models to the functional classification of biosequences and to calculate alignment-free distances for phylogenetic purposes. We released the version 2.0 of the software that can be freely downloaded from http://ti2biop.sourceforge.net/.
Keywords
2D graphs
Topological indices
Alignment-free models
Phylogenetics
Manuscript
3-TI2BioP_Software_Aguero_Chapin_G.pdf
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