SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14110%2F14%3A00076179" target="_blank" >RIV/00216224:14110/14:00076179 - isvavai.cz</a>

Alternative codes found

RIV/68081766:_____/14:00422473

Result on the web

<a href="http://dx.doi.org/10.1093/bioinformatics/btt727" target="_blank" >http://dx.doi.org/10.1093/bioinformatics/btt727</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/bioinformatics/btt727" target="_blank" >10.1093/bioinformatics/btt727</a>

Result language

angličtina

Original language name

SigHunt: Horizontal Gene Transfer Finder Optimized for Eukaryotic Genomes

Original language 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 inprokaryotes, 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 compositionof 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 alocal kernel density estimate of the 4-mer frequency.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CE - Biochemistry

OECD FORD branch

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Project

<a href="/en/project/GAP506%2F12%2F1064" target="_blank" >GAP506/12/1064: Bat adaptations to the fungal disease geomycosis</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2014

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

BIOINFORMATICS

ISSN

1367-4803

e-ISSN

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Volume of the periodical

30

Issue of the periodical within the volume

8

Country of publishing house

GB - UNITED KINGDOM

Number of pages

6

Pages from-to

1081-1086

UT code for WoS article

000335001000005

EID of the result in the Scopus database

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