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Titolo:
Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier
Autore:
Sandberg, R; Winberg, G; Branden, CI; Kaske, A; Ernberg, I; Coster, J;
Indirizzi:
Karolinska Inst, Ctr Microbiol & Tumor Biol, S-17177 Stockholm, Sweden Karolinska Inst Stockholm Sweden S-17177 Biol, S-17177 Stockholm, Sweden Virtual Genet Lab AB, S-17177 Stockholm, Sweden Virtual Genet Lab AB Stockholm Sweden S-17177 S-17177 Stockholm, Sweden
Titolo Testata:
GENOME RESEARCH
fascicolo: 8, volume: 11, anno: 2001,
pagine: 1404 - 1409
SICI:
1088-9051(200108)11:8<1404:CWCISS>2.0.ZU;2-4
Fonte:
ISI
Lingua:
ENG
Soggetto:
HORIZONTAL GENE-TRANSFER; BACTERIAL GENOMES; DNA-SEQUENCES; DINUCLEOTIDE; SIGNATURE;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
21
Recensione:
Indirizzi per estratti:
Indirizzo: Sandberg, R Karolinska Inst, Ctr Microbiol & Tumor Biol, S-17177 Stockholm, Sweden Karolinska Inst Stockholm Sweden S-17177 7 Stockholm, Sweden
Citazione:
R. Sandberg et al., "Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier", GENOME RES, 11(8), 2001, pp. 1404-1409

Abstract

Bacterial genomes have diverged during evolution, resulting in clearcut differences in their nucleotide ge composition, such as their GC content. Theanalysis of complete sequences of bacterial genomes also reveals the presence of nonrandom. sequence variation, manifest in the frequency profile of specific short oligonucleotides. These frequency profiles constitute highlyspecific genomic signatures. Based on these differences in oligonucleotidefrequency between bacterial genomes, we investigated the possibility of predicting the genome of origin for a specific genomic sequence. To this end,we developed a naive Bayesian classifier and systematically analyzed 28 eubacterial and archaeal genomes. We found that sequences as short as 400 bases could be correctly classified with an accuracy of 85%. We then applied the classifier to the identification of horizontal gene transfer events In whole-genome sequences and demonstrated the validity of our approach by correctly predicting the transfer of both the superoxide dismutase (sodC) and the bioC gene from Haemophilus influenzae to Neisseria meningitis, correctlyidentifying both the donor and recipient species. We believe that this classification methodology could be a valuable tool in biodiversity studies.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 02/04/20 alle ore 22:13:40