title: MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification.
abstract: BACKGROUND
  Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- and character-based methods.
  
  
  RESULTS
  We propose a supervised method based on a genetic algorithm to identify small genomic subsequences that discriminate among different species. The method identifies multiple subsequences of bounded length with the same information power in a given genomic region. The algorithm has been successfully evaluated through its integration into a rule-based classification framework and applied to three different biological data sets: Influenza, Polyoma, and Rhino virus sequences.
  
  
  CONCLUSIONS
  We discover a large number of small subsequences that can be used to identify each virus type with high accuracy and low computational time, and moreover help to characterize different genomic regions. Bounding their length to 20, our method found 1164 characterizing subsequences for all the Influenza virus subtypes, 194 for all the Polyoma viruses, and 11 for Rhino viruses. The abundance of small separating subsequences extracted for each genomic region may be an important support for quick and robust virus identification. Finally, useful biological information can be derived by the relative location and abundance of such subsequences along the different regions.
authors.affiliation: Institute of Systems Analysis and Computer Science A. Ruberti (IASI), National Research Council (CNR), Via dei Taurini 19, Rome, 00185 Italy.
authors.forename: Giulia
authors.identifier: 0000-0002-3354-8203
authors.initials: G
authors.lastname: Fiscon
authors.affiliation: Institute of Systems Analysis and Computer Science A. Ruberti (IASI), National Research Council (CNR), Via dei Taurini 19, Rome, 00185 Italy.|Department of Engineering, Uninettuno International University, Corso Vittorio Emanuele II 39, Rome, 00186 Italy.
authors.forename: Emanuel
authors.initials: E
authors.lastname: Weitschek
authors.affiliation: Department of Infectious Diseases, Istituto Superiore di Sanita, Viale Regina Margherita 299, Rome, 00161 Italy.|Public Health and Infectious Diseases, Sapienza University, Piazzale Aldo Moro 5, Rome, 00185 Italy.
authors.forename: Eleonora
authors.initials: E
authors.lastname: Cella
authors.affiliation: Department of Infectious Diseases, Istituto Superiore di Sanita, Viale Regina Margherita 299, Rome, 00161 Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Lo Presti
authors.affiliation: Department of Infectious Diseases, Istituto Superiore di Sanita, Viale Regina Margherita 299, Rome, 00161 Italy.|Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, Rome, 00133 Italy.
authors.forename: Marta
authors.initials: M
authors.lastname: Giovanetti
authors.affiliation: Foundation of Technical Education, Sulaimaniyah, Kurdistan Region, Iraq.
authors.forename: Muhammed
authors.initials: M
authors.lastname: Babakir-Mina
authors.affiliation: Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, Viale Oxford 81, Rome, 00133 Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Ciotti
authors.affiliation: Institute of Systems Analysis and Computer Science A. Ruberti (IASI), National Research Council (CNR), Via dei Taurini 19, Rome, 00185 Italy.|Department of Infectious Diseases, Istituto Superiore di Sanita, Viale Regina Margherita 299, Rome, 00161 Italy.
authors.forename: Massimo
authors.initials: M
authors.lastname: Ciccozzi
authors.affiliation: Virology Laboratory, Department of Molecular Medicine, Sapienza University, Viale di Porta Tiburtina 2, Rome, 00185 Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Pierangeli
authors.affiliation: Institute of Systems Analysis and Computer Science A. Ruberti (IASI), National Research Council (CNR), Via dei Taurini 19, Rome, 00185 Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Bertolazzi
authors.affiliation: Institute of Systems Analysis and Computer Science A. Ruberti (IASI), National Research Council (CNR), Via dei Taurini 19, Rome, 00185 Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Felici
keywords: Classification of genomic sequences; Extraction of multiple classification models; Genetic algorithms; Supervised learning