SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes

JAROŇ, Kamil, Jiří MORAVEC a Natália MARTÍNKOVÁ. SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes. BIOINFORMATICS. Oxford: Oxford University Press, 2014, roč. 30, č. 8, s. 1081-1086. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btt727.

Základní údaje

• Originální název: SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes
• Autoři: JAROŇ, Kamil (203 Česká republika, domácí), Jiří MORAVEC (203 Česká republika, domácí) a Natália MARTÍNKOVÁ (703 Slovensko, garant, domácí).
• Vydání: BIOINFORMATICS, Oxford, Oxford University Press, 2014, 1367-4803.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Článek v odborném periodiku
• Obor: 10600 1.6 Biological sciences
• Stát vydavatele: Velká Británie a Severní Irsko
• Utajení: není předmětem státního či obchodního tajemství
• Impakt faktor: Impact factor: 4.981
• Kód RIV: RIV/00216224:14110/14:00076179
• Organizační jednotka: Lékařská fakulta
• Doi: http://dx.doi.org/10.1093/bioinformatics/btt727
• UT WoS: 000335001000005
• Klíčová slova anglicky: FUNGUS ASPERGILLUS-FUMIGATUS; CRYPTOSPORIDIUM-PARVUM; SEQUENCE; EVOLUTION; IDENTIFICATION; ISLANDS; ECOLOGY
• Štítky: EL OK
• Příznaky: Mezinárodní význam, Recenzováno

Anotace

Motivation: Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead. Results: We present a surrogate method that investigates nucleotide base composition of the DNA sequence in a eukaryotic genome and identifies putative GIs. We calculate a genomic signature as a vector of tetranucleotide (4-mer) frequencies using a sliding window approach. Extending the neighbourhood of the sliding window, we establish a local kernel density estimate of the 4-mer frequency. We score the number of 4-mer frequencies in the sliding window that deviate from the credibility interval of their local genomic density using a newly developed discrete interval accumulative score (DIAS). To further improve the effectiveness of DIAS, we select informative 4-mers in a range of organisms using the tetranucleotide quality score developed herein. We show that the SigHunt method is computationally efficient and able to detect GIs in eukaryotic genomes that represent nonameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition.