Current Bioinformatics

Yi-Ping Phoebe Chen
Department of Computer Science and Information Technology
La Trobe University
Melbourne
Australia

Back

S2SNet: A Tool for Transforming Characters and Numeric Sequences into Star Network Topological Indices in Chemoinformatics, Bioinformatics, Biomedical, and Social-Legal Sciences

Author(s): Cristian R. Munteanu, Alexandre L. Magalhaes, Aliuska Duardo-Sanchez, Alejandro Pazos, Humberto Gonzalez-Diaz.

Abstract:

The study of complex systems such as proteins/DNA/RNA or dynamics of tax law systems can be carried out with the complex network theory. This allows the numerical quantification of the significant information contained by the sequences of amino acids, nucleotides or types of tax laws. In this paper we describe S2SNet, a new Python tool with a graphical user interface that can transform any sequence of characters or numbers into series of invariant star network topological indices. The application is based on Python reusable processing procedures that perform different functions such as reading sequence data, transforming numerical series into character sequences, changing letter codification of strings and drawing the star networks of each sequence using Graphviz package as graphical back-end. S2SNet was previously used to obtain classification models for natural/random proteins, breast/colon/prostate cancer-related proteins, DNA sequences of mycobacterial promoters and for early detection of diseases and drug-induced toxicities using the blood serum proteome mass spectrum. In order to show the extended practical potential of S2SNet, this work presents several examples of application for proteins, DNA/RNA, blood proteome mass spectra and time evolution of the financial law recurrence. The obtained topological indices can be used to characterize systems by creating classification models, clustering or pattern search with statistical, Neural Network or Machine Learning methods. The free availability of S2SNet, the flexibility of analyzing diverse systems and the Python portability make it an ideal tool in fields such as Bioinformatics, Proteomics, Genomics, and Biomedicine or Social, Economic and Political Sciences.

Keywords: Complex network, financial law network, graph indices, interaction, network, protein, python application, social network.

Order Reprints Order Eprints Rights & PermissionsPrintExport

Article Details

VOLUME: 8
ISSUE: 4
Year: 2013
Page: [429 - 437]
Pages: 9
DOI: 10.2174/1574893611308040005