title: GIPSy: Genomic island prediction software.
abstract: Bacteria are highly diverse organisms that are able to adapt to a broad range of environments and hosts due to their high genomic plasticity. Horizontal gene transfer plays a pivotal role in this genome plasticity and in evolution by leaps through the incorporation of large blocks of genome sequences, ordinarily known as genomic islands (GEIs). GEIs may harbor genes encoding virulence, metabolism, antibiotic resistance and symbiosis-related functions, namely pathogenicity islands (PAIs), metabolic islands (MIs), resistance islands (RIs) and symbiotic islands (SIs). Although many software for the prediction of GEIs exist, they only focus on PAI prediction and present other limitations, such as complicated installation and inconvenient user interfaces. Here, we present GIPSy, the genomic island prediction software, a standalone and user-friendly software for the prediction of GEIs, built on our previously developed pathogenicity island prediction software (PIPS). We also present four application cases in which we crosslink data from literature to PAIs, MIs, RIs and SIs predicted by GIPSy. Briefly, GIPSy correctly predicted the following previously described GEIs: 13 PAIs larger than 30kb in Escherichia coli CFT073; 1 MI for Burkholderia pseudomallei K96243, which seems to be a miscellaneous island; 1 RI of Acinetobacter baumannii AYE, named AbaR1; and, 1 SI of Mesorhizobium loti MAFF303099 presenting a mosaic structure. GIPSy is the first life-style-specific genomic island prediction software to perform analyses of PAIs, MIs, RIs and SIs, opening a door for a better understanding of bacterial genome plasticity and the adaptation to new traits.
authors.affiliation: Department of Immunology, Microbiology and Parasitology, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil; Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. Electronic address: siomars@gmail.com.
authors.forename: Siomar C
authors.initials: SC
authors.lastname: Soares
authors.affiliation: Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany. Electronic address: hakan.geyik@uni-bielefeld.de.
authors.forename: Hakan
authors.initials: H
authors.lastname: Geyik
authors.affiliation: Department of Genetics, Federal University of Pará, Belém, Pará, Brazil. Electronic address: rommelramos@ufpa.br.
authors.forename: Rommel T J
authors.initials: RT
authors.lastname: Ramos
authors.affiliation: Department of Genetics, Federal University of Pará, Belém, Pará, Brazil. Electronic address: pablogomesdesa@gmail.com.
authors.forename: Pablo H C G
authors.initials: PH
authors.lastname: de Sá
authors.affiliation: Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Computational Biology laboratory, Institute for Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark. Electronic address: eudesgvb@gmail.com.
authors.forename: Eudes G V
authors.initials: EG
authors.lastname: Barbosa
authors.affiliation: Computational Biology laboratory, Institute for Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark. Electronic address: jan.baumbach@imada.sdu.dk.
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
authors.affiliation: AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. Electronic address: figueiredoh@yahoo.com.
authors.forename: Henrique C P
authors.initials: HC
authors.lastname: Figueiredo
authors.affiliation: Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. Electronic address: miyoshi@icb.ufmg.br.
authors.forename: Anderson
authors.initials: A
authors.lastname: Miyoshi
authors.affiliation: Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany. Electronic address: tauch@cebitec.uni-bielefeld.de.
authors.forename: Andreas
authors.initials: A
authors.lastname: Tauch
authors.affiliation: Department of Genetics, Federal University of Pará, Belém, Pará, Brazil. Electronic address: asilva@ufpa.br.
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
authors.affiliation: Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. Electronic address: vascoariston@gmail.com.
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
mesh_terms: D004926:Escherichia coli / Q000235:genetics; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D044404:Genomic Islands / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D012984:Software
keywords: Genome plasticity; Genomic islands; Horizontal gene transfer; Metabolic islands; Pathogenicity islands; Resistance islands; Symbiotic islands