loading
Papers

Research.Publish.Connect.

Paper

Paper Unlock

Authors: Oliver Bezuidt ; Kingdom Mncube and Oleg N. Reva

Affiliation: University of Pretoria, South Africa

ISBN: 978-989-8425-90-4

Keyword(s): Genome linguistics, k-Mer statistics, Oligonucleotide usage pattern, Genomic island, Horizontal gene exchange, Pathogenicity.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Artificial Intelligence ; Bioinformatics ; Biomedical Engineering ; Genomics and Proteomics ; Sequence Analysis ; Soft Computing ; Visualization

Abstract: With more sequences of complete bacterial genomes getting public availability the approaches of genome comparison by frequencies of oligonucleotides (k-mers) known also as the genome linguistics are becoming popular and practical to resolve problems which can not be tackled by the traditional sequence comparison tools. In this work we present several innovative approaches based on k-mer statistics for detection of inserts of genomic islands and tracing down the ontological links and origins of mobile genetic elements. 637 bacterial genomes were analyzed by SeqWord Sniffer program that has detected 2,622 putative genomic islands. These genomic islands were clustered by DNA compositional similarity. A stratigraphic analysis was introduced that allows distinguishing between new and old genomic inserts. A method of reconstruction of donor-recipient relations between micro-organisms was proposed. The strain E. coli TY-2,482 isolated from the latest deadly outbreak of a haemorrhagic infecti on in Europe in 2011 was used for the case study. It was shown that this strain appeared on an intersection of two independent fluxes of horizontal gene exchange, one of which is a conventional for Enterobacteria stream of vectors generated in marine gamma-Proteobacteria; and the second is a new channel of antibiotic resistance genomic islands originated from environmental beta-Proteobacteria. (More)

PDF ImageFull Text

Download
CC BY-NC-ND 4.0

Sign In Guest: Register as new SciTePress user now for free.

Sign In SciTePress user: please login.

PDF ImageMy Papers

You are not signed in, therefore limits apply to your IP address 18.210.22.132

In the current month:
Recent papers: 100 available of 100 total
2+ years older papers: 200 available of 200 total

Paper citation in several formats:
Bezuidt, O.; Mncube, K. and N. Reva, O. (2012). APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 118-123. DOI: 10.5220/0003704201180123

@conference{bioinformatics12,
author={Oliver Bezuidt. and Kingdom Mncube. and Oleg N. Reva.},
title={APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={118-123},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003704201180123},
isbn={978-989-8425-90-4},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange
SN - 978-989-8425-90-4
AU - Bezuidt, O.
AU - Mncube, K.
AU - N. Reva, O.
PY - 2012
SP - 118
EP - 123
DO - 10.5220/0003704201180123

Login or register to post comments.

Comments on this Paper: Be the first to review this paper.