In this paper we present an application of the neural gas network to the classification of the DNA barcode sequences. The proposed method is based on the identification of distinctive words, extracted from the spectral representation of DNA sequences. In particular we calculated the "signatures" that are a characteristic of the DNA sequence at different taxonomic levels. In order to demonstrate the efficacy of the proposed method, we tested it over 10 real barcode datasets belonging to different animalia species, provided by on-line resource Barcode of Life Database (BOLD). © Springer-Verlag Berlin Heidelberg 2013.

Analysis of DNA barcode sequences using neural gas and spectral representation

Fiannaca A;La Rosa M;Rizzo R;Urso A
2013

Abstract

In this paper we present an application of the neural gas network to the classification of the DNA barcode sequences. The proposed method is based on the identification of distinctive words, extracted from the spectral representation of DNA sequences. In particular we calculated the "signatures" that are a characteristic of the DNA sequence at different taxonomic levels. In order to demonstrate the efficacy of the proposed method, we tested it over 10 real barcode datasets belonging to different animalia species, provided by on-line resource Barcode of Life Database (BOLD). © Springer-Verlag Berlin Heidelberg 2013.
2013
Istituto di Calcolo e Reti ad Alte Prestazioni - ICAR
Istituto di Calcolo e Reti ad Alte Prestazioni - ICAR
978-3-642-41015-4
Alignment-free
DNA barcode
DNA k-mer
Neural gas
Spectral representation
File in questo prodotto:
Non ci sono file associati a questo prodotto.

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.14243/261724
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 10
  • ???jsp.display-item.citation.isi??? ND
social impact