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Protocols

GIPSy specifications

Information


Unique identifier OMICS_24982
Name GIPSy
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A genome file.
Input format embl, genbank
Output data A list of all genes with information on CDS location and CDS product.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.1.2
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Siomar C. Soares
  • person_outline Rommel Thiago Jucá Ramos
  • person_outline Hakan Geyik
  • person_outline Pablo de Sa
  • person_outline Vasco Azevedo

Publication for GIPSy

GIPSy citations

 (8)
library_books

Genomic Architecture of the Two Cold Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome

2018
Genome Biol Evol
PMCID: 5833320
PMID: 29438502
DOI: 10.1093/gbe/evy029

[…] rings generated by the software, BRIG. Synteny between the genomes was analysed on the software Artemis Comparison Tool (ACT) v.13.0.0 (). Genomic Islands (GIs) of E. antarcticum B7 were predicted by GIPSy (). Four types of islands were predicted: Resistance Island (RI), Pathogenicity Island (PAI), Symbiotic Island (SI), and Metabolic Island (MI). The thermophilic specie Exiguobacterium AT1b was u […]

call_split

Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo

2017
PLoS One
PMCID: 5406005
PMID: 28445543
DOI: 10.1371/journal.pone.0176347
call_split See protocol

[…] Pathogenicity islands (PAIs) were predicted by GIPSy []. All 11 genomes were individually compared to the C. glutamicum ATCC1302 genome (NC_006958.1), a non-pathogenic strain. DoubleACT v2 (http://www.hpa-bioinfotools.org.uk/pise/double_act.html) […]

call_split

Analyses of the probiotic property and stress resistance related genes of Lactococcus lactis subsp. lactis NCDO 2118 through comparative genomics and in vitro assays

2017
PLoS One
PMCID: 5383145
PMID: 28384209
DOI: 10.1371/journal.pone.0175116
call_split See protocol

[…] The genome plasticity analyses were performed by searching for horizontally acquired regions such as genomic islands and phage sequences. The genomic islands were searched using the software GIPSy: Genomic Island Prediction Software [], which updates the methodology of the software PIPS: Pathogenicity Island Prediction Software. Briefly, GIPSy performs the prediction of four different cla […]

library_books

An In Silico Identification of Common Putative Vaccine Candidates against Treponema pallidum: A Reverse Vaccinology and Subtractive Genomics Based Approach

2017
Int J Mol Sci
PMCID: 5343936
PMID: 28216574
DOI: 10.3390/ijms18020402

[…] arget protein were determined using UniProt []. The biochemical pathway of these proteins were checked using KEGG (Kyoto Encyclopedia of Genes and Genomes) [], SurfG+ software [], and virulence using GIPSy []. The final list of targets was based on 12 criteria, as described earlier in [,]. […]

library_books

Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics

2017
PLoS One
PMCID: 5268413
PMID: 28125655
DOI: 10.1371/journal.pone.0170676

[…] The PAIs and RIs were identified with GIPSy v1.1.2 software []. C. glutamicum ATCC 13032 was used as a non-pathogenic strain of reference. The complete lists of virulence factors, resistance genes, locations and composition of PAIs and RI […]

library_books

Pathoadaptive Mutations of Escherichia coli K1 in Experimental Neonatal Systemic Infection

2016
PLoS One
PMCID: 5115809
PMID: 27861552
DOI: 10.1371/journal.pone.0166793

[…] elvetOptimiser []. xBASE was used to predict protein coding sequences (CDS) and tRNA genes []. Functional annotation of CDS was performed by manual BLAST searches and genomic features identified with GIPSy software []. The E. coli A192 draft genome was compared with published E. coli genome sequences using Artemis Comparison Tool [] and BLAST ring image generator []. To assess the evolutionary rel […]

Citations

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GIPSy institution(s)
Department of Immunology, Microbiology and Parasitology, Federal University of Triangulo Mineiro, Uberaba, Brazil; Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Brazil; Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Department of Genetics, Federal University of Pará, Belém, Brazil; Computational Biology laboratory, Institute for Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark; AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, Brazil
GIPSy funding source(s)
Supported by Bielefeld University (Germany) and a post-doc scholarship (grant number 151262/2013-6).

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