{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T12:10:14Z","timestamp":1783512614018,"version":"3.55.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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 non-ameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition.<\/jats:p>\n               <jats:p>Availability and implementation: Source code and scripts freely available for download at http:\/\/www.iba.muni.cz\/index-en.php?pg=research\u2013data-analysis-tools\u2013sighunt are implemented in C and R and are platform-independent.<\/jats:p>\n               <jats:p>Contact: \u00a0376090@mail.muni.cz or martinkova@ivb.cz<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt727","type":"journal-article","created":{"date-parts":[[2013,12,27]],"date-time":"2013-12-27T01:10:37Z","timestamp":1388106637000},"page":"1081-1086","source":"Crossref","is-referenced-by-count":29,"title":["SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes"],"prefix":"10.1093","volume":"30","author":[{"given":"Kamil S.","family":"Jaron","sequence":"first","affiliation":[{"name":"1 Institute of Biostatistics and Analyses, Masaryk University and 2Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji\u0159\u00ed C.","family":"Moravec","sequence":"additional","affiliation":[{"name":"1 Institute of Biostatistics and Analyses, Masaryk University and 2Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nat\u00e1lia","family":"Mart\u00ednkov\u00e1","sequence":"additional","affiliation":[{"name":"1 Institute of Biostatistics and Analyses, Masaryk University and 2Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic"},{"name":"1 Institute of Biostatistics and Analyses, Masaryk University and 2Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,12,25]]},"reference":[{"key":"2023012710484236600_btt727-B1","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1126\/science.1094786","article-title":"Complete genome sequence of the apicomplexan, Cryptosporidium parvum","volume":"304","author":"Abrahamsen","year":"2004","journal-title":"Science"},{"key":"2023012710484236600_btt727-B2","doi-asserted-by":"crossref","first-page":"2185","DOI":"10.1126\/science.287.5461.2185","article-title":"The genome sequence of Drosophila melanogaster","volume":"287","author":"Adams","year":"2000","journal-title":"Science"},{"key":"2023012710484236600_btt727-B3","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1126\/science.1101156","article-title":"The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism","volume":"306","author":"Armbrust","year":"2004","journal-title":"Science"},{"key":"2023012710484236600_btt727-B4","doi-asserted-by":"crossref","first-page":"e144","DOI":"10.1093\/nar\/gkr735","article-title":"Towards an accurate identification of mosaic genes and partial horizontal gene transfers","volume":"39","author":"Boc","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012710484236600_btt727-B5","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1111\/mec.12170","article-title":"The impact of transposable elements in environmental adaptation","volume":"22","author":"Casacuberta","year":"2013","journal-title":"Mol. 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