A C + + computational environment for biomolecular sequence management

The wide production of biomolecular data of the last 30 years, mainly due to the rapid evolving of technologies as well as to the accomplishment of the Genome Projects, led to the necessity of appropriate computational approaches for data storage, manipulation and analyses, giving place to a fast evolving area of Biology: Computational Biology or Bioinformatics.

We propose here a new method for the storage of the sequences and their analyses using the C + + programming language, checking the effectiveness of an object oriented approach for new models, suitable to manage data representation and analyses, to improve the efficiency of computational methodologies to solve problems of general interest in bioinformatics. We developed a framework with the aim to decrease the computational costs for the storage and some basic manipulations of nucleic acid sequences. The remarkable reduction of memory requirements with no loss of efficiency makes this approach a first well promising step in order to get a more efficient environment for the manipulation and the management of nucleic acid data sets, in a field of research with hard challenges for Computer and Life Sciences.

Authors and Affiliations

1. Dipartimento di Biologia Strutturale e Funzionale, University of Naples Federico II, Via Mezzocannone 8, 80134, Napoli, Italy

   M. L. Chiusano

2. Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1111 Yata, Mishima-Shi, 411-8540, Shizuoka, Japan

   Takashi Gojobori

3. Japan Biological Information Research Center (BIRC/JBIRC), National Institute of Advanced Industrial Science and Technology, AIST Tokyo, Waterfront Bio-IT Research Building 7F, 2-42 Aomi, 135-0064, Koto-ku, Tokyo, Japan

   G. Toraldo

4. Dipartimento di Ingegneria Agraria e Agronomia del Territorio, University of Naples Federico II, Via Universitá 100, 80055, Portici, Napoli, Italy

   G. Toraldo

Corresponding author

Correspondence to G. Toraldo.

Mathematics Subject Classification:

68U99

G. Toraldo, via Universita’ 100, 80055 Portici, Napoli, Italy

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