Počet záznamů: 1  

SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes

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    SYSNO ASEP0422473
    Druh ASEPJ - Článek v odborném periodiku
    Zařazení RIVJ - Článek v odborném periodiku
    Poddruh JČlánek ve WOS
    NázevSigHunt: horizontal gene transfer finder optimized for eukaryotic genomes
    Tvůrce(i) Jaron, K. S. (CZ)
    Moravec, J. C. (CZ)
    Martínková, Natália (UBO-W) RID, ORCID, SAI
    Celkový počet autorů3
    Zdroj.dok.Bioinformatics. - : Oxford University Press - ISSN 1367-4803
    Roč. 30, č. 8 (2014), s. 1081-1086
    Poč.str.6 s.
    Jazyk dok.eng - angličtina
    Země vyd.GB - Velká Británie
    Klíč. slovafungus Aspergillus fumigatus ; Cryptosporidium parvum ; sequence ; evolution ; identification ; islands ; ecology
    Vědní obor RIVEB - Genetika a molekulární biologie
    CEPGAP506/12/1064 GA ČR - Grantová agentura ČR
    Institucionální podporaUBO-W - RVO:68081766
    UT WOS000335001000005
    EID SCOPUS84898910228
    DOI10.1093/bioinformatics/btt727
    AnotaceMotivation: 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.
    PracovištěÚstav biologie obratlovců
    KontaktHana Slabáková, slabakova@ivb.cz, Tel.: 543 422 524
    Rok sběru2015
Počet záznamů: 1  

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