PIPS: pathogenicity island prediction software.

PloS One
Siomar C SoaresVasco Azevedo

Abstract

The adaptability of pathogenic bacteria to hosts is influenced by the genomic plasticity of the bacteria, which can be increased by such mechanisms as horizontal gene transfer. Pathogenicity islands play a major role in this type of gene transfer because they are large, horizontally acquired regions that harbor clusters of virulence genes that mediate the adhesion, colonization, invasion, immune system evasion, and toxigenic properties of the acceptor organism. Currently, pathogenicity islands are mainly identified in silico based on various characteristic features: (1) deviations in codon usage, G+C content or dinucleotide frequency and (2) insertion sequences and/or tRNA genetic flanking regions together with transposase coding genes. Several computational techniques for identifying pathogenicity islands exist. However, most of these techniques are only directed at the detection of horizontally transferred genes and/or the absence of certain genomic regions of the pathogenic bacterium in closely related non-pathogenic species. Here, we present a novel software suite designed for the prediction of pathogenicity islands (pathogenicity island prediction software, or PIPS). In contrast to other existing tools, our approach is cap...Continue Reading

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Citations

Jan 30, 2013·Critical Reviews in Microbiology·Mehari Tesfazgi MebrhatuAbram Aertsen
Dec 24, 2015·BMC Genomics·Henrique C P FigueiredoCarlos A G Leal
Dec 4, 2012·Microbial Biotechnology·Rommel Thiago Jucá RamosArtur Silva
Mar 26, 2016·Genome Announcements·Carlos Leonardo de A AraújoAdriana R Carneiro
Sep 17, 2015·Journal of Biotechnology·Siomar C SoaresVasco Azevedo
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Apr 14, 2016·Journal of Medical Microbiology·Andrea de Fátima Silva RezendeSibele Borsuk
Jul 10, 2019·Microbial Biotechnology·Thiago Doria BarralRicardo Dias Portela
Jun 6, 2018·Briefings in Bioinformatics·Claire BertelliFiona S L Brinkman
Apr 26, 2017·Frontiers in Microbiology·Krupa M ParmarRavindra Pal Singh
Jan 12, 2019·Frontiers in Genetics·Antonio Camilo da Silva FilhoJeroniza Nunes Marchaukoski
Aug 17, 2019·Royal Society Open Science·Thaís Cristina Vilela RodriguesSiomar de Castro Soares

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Datasets Mentioned

BETA
BX248353
–
BX927147
CP001809
CP001829
AE014075
U00096

Software Mentioned

genemark
Artemis
DIMOB
ColomboSIGI
- DIMOB
Perl script
IslandViewer
tRNAscan
tRNAcc
Annotatiohmm

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