Attributes | Values |
---|
rdf:type
| |
Description
| - 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
| |
http://linked.open...iv/cisloPeriodika
| |
http://linked.open...vai/riv/dodaniDat
| |
http://linked.open...aciTvurceVysledku
| |
http://linked.open.../riv/druhVysledku
| |
http://linked.open...iv/duvernostUdaju
| |
http://linked.open...titaPredkladatele
| |
http://linked.open...dnocenehoVysledku
| |
http://linked.open...ai/riv/idVysledku
| - RIV/00216224:14110/14:00076179
|
http://linked.open...riv/jazykVysledku
| |
http://linked.open.../riv/klicovaSlova
| - FUNGUS ASPERGILLUS-FUMIGATUS; CRYPTOSPORIDIUM-PARVUM; SEQUENCE; EVOLUTION; IDENTIFICATION; ISLANDS; ECOLOGY (en)
|
http://linked.open.../riv/klicoveSlovo
| |
http://linked.open...odStatuVydavatele
| - GB - Spojené království Velké Británie a Severního Irska
|
http://linked.open...ontrolniKodProRIV
| |
http://linked.open...i/riv/nazevZdroje
| |
http://linked.open...in/vavai/riv/obor
| |
http://linked.open...ichTvurcuVysledku
| |
http://linked.open...cetTvurcuVysledku
| |
http://linked.open...vavai/riv/projekt
| |
http://linked.open...UplatneniVysledku
| |
http://linked.open...v/svazekPeriodika
| |
http://linked.open...iv/tvurceVysledku
| - Moravec, Jiří
- Martínková, Natália
- Jaroň, Kamil
|
http://linked.open...ain/vavai/riv/wos
| |
issn
| |
number of pages
| |
http://bibframe.org/vocab/doi
| - 10.1093/bioinformatics/btt727
|
http://localhost/t...ganizacniJednotka
| |