SigHunt: Horizontal Gene Transfer Finder Optimized for
Eukaryotic Genomes

J 2014

SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes

JAROŇ, Kamil; Jiří MORAVEC a Natália MARTÍNKOVÁ

Základní údaje

Originální název

SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes

Autoři

JAROŇ, Kamil; Jiří MORAVEC a Natália MARTÍNKOVÁ

Vydání

BIOINFORMATICS, Oxford, Oxford University Press, 2014, 1367-4803

Další údaje

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

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14110/14:00076179

Organizační jednotka

Lékařská fakulta

Klíčová slova anglicky

FUNGUS ASPERGILLUS-FUMIGATUS; CRYPTOSPORIDIUM-PARVUM; SEQUENCE; EVOLUTION; IDENTIFICATION; ISLANDS; ECOLOGY

Štítky

EL OK

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 10. 2. 2015 10:58, Ing. Mgr. Věra Pospíšilíková

Anotace

V originále

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.

Citovat

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://doi.org/10.1093/bioinformatics/btt727.

@article{1195388,
   author = {Jaroň, Kamil and Moravec, Jiří and Martínková, Natália},
   article_location = {Oxford},
   article_number = {8},
   doi = {https://doi.org/10.1093/bioinformatics/btt727},
   keywords = {FUNGUS ASPERGILLUS-FUMIGATUS; CRYPTOSPORIDIUM-PARVUM; SEQUENCE; EVOLUTION; IDENTIFICATION; ISLANDS; ECOLOGY},
   language = {eng},
   issn = {1367-4803},
   journal = {BIOINFORMATICS},
   title = {SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes},
   volume = {30},
   year = {2014}
}

TY  - JOUR
ID  - 1195388
AU  - Jaroň, Kamil - Moravec, Jiří - Martínková, Natália
PY  - 2014
TI  - SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes
JF  - BIOINFORMATICS
VL  - 30
IS  - 8
SP  - 1081-1086
EP  - 1081-1086
PB  - Oxford University Press
SN  - 13674803
KW  - FUNGUS ASPERGILLUS-FUMIGATUS
KW  - CRYPTOSPORIDIUM-PARVUM
KW  - SEQUENCE
KW  - EVOLUTION
KW  - IDENTIFICATION
KW  - ISLANDS
KW  - ECOLOGY
N2  - 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.
ER  -

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

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