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SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes
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SYSNO ASEP 0422473 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes Author(s) Jaron, K. S. (CZ)
Moravec, J. C. (CZ)
Martínková, Natália (UBO-W) RID, ORCID, SAINumber of authors 3 Source Title Bioinformatics. - : Oxford University Press - ISSN 1367-4803
Roč. 30, č. 8 (2014), s. 1081-1086Number of pages 6 s. Language eng - English Country GB - United Kingdom Keywords fungus Aspergillus fumigatus ; Cryptosporidium parvum ; sequence ; evolution ; identification ; islands ; ecology Subject RIV EB - Genetics ; Molecular Biology R&D Projects GAP506/12/1064 GA ČR - Czech Science Foundation (CSF) Institutional support UBO-W - RVO:68081766 UT WOS 000335001000005 EID SCOPUS 84898910228 DOI 10.1093/bioinformatics/btt727 Annotation Motivation: Genomic islands 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 employed instead. Results: We present a surrogate method that investigates nucleotide base composition of the DNA sequence in a eukaryotic genome and identifies putative genomic islands. We calculate a genomic signature as a vector of tetranucleotide (4-mer) frequencies utilizing 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 (TES) developed herein. We show that the SigHunt method is computationally efficient and able to detect genomic islands in eukaryotic genomes that represent non-ameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition. Availability: Source code and scripts freely available for download at http://www.iba.muni.cz/index-en.php?pg=research--data-analysistools-- sighunt are implemented in C and R and are platformindependent. Workplace Institute of Vertebrate Biology Contact Hana Slabáková, slabakova@ivb.cz, Tel.: 543 422 524 Year of Publishing 2015
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