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  • 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.
  • 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. (en)
Title
  • SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes
  • SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes (en)
skos:prefLabel
  • SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes
  • SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes (en)
skos:notation
  • RIV/00216224:14110/14:00076179!RIV15-MSM-14110___
http://linked.open...avai/riv/aktivita
http://linked.open...avai/riv/aktivity
  • I, P(GAP506/12/1064)
http://linked.open...iv/cisloPeriodika
  • 8
http://linked.open...vai/riv/dodaniDat
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http://linked.open...dnocenehoVysledku
  • 44796
http://linked.open...ai/riv/idVysledku
  • RIV/00216224:14110/14:00076179
http://linked.open...riv/jazykVysledku
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  • FUNGUS ASPERGILLUS-FUMIGATUS; CRYPTOSPORIDIUM-PARVUM; SEQUENCE; EVOLUTION; IDENTIFICATION; ISLANDS; ECOLOGY (en)
http://linked.open.../riv/klicoveSlovo
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  • GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV
  • [18E24E41462F]
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  • BIOINFORMATICS
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http://linked.open...v/svazekPeriodika
  • 30
http://linked.open...iv/tvurceVysledku
  • Moravec, Jiří
  • Martínková, Natália
  • Jaroň, Kamil
http://linked.open...ain/vavai/riv/wos
  • 000335001000005
issn
  • 1367-4803
number of pages
http://bibframe.org/vocab/doi
  • 10.1093/bioinformatics/btt727
http://localhost/t...ganizacniJednotka
  • 14110
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