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

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

Document Type: Research Article

Publication date: September 1, 2013

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  • Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a wide range of the integration of biology with computer and information science.

    The journal focuses on reviews on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.

    Current Bioinformatics is an essential journal for all academic and industrial researchers who want expert knowledge on all major advances in bioinformatics.
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