GIPSy statistics

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Associated diseases

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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 in pipeline

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

[…] unique islands from mb336 were also present in the genome of the strain mb122 and other isolates from california (), which suggest that the conservation of these pais is higher than that observed by gipsy. these pais contained important virulence factors for c. pseudotuberculosis, such as the cluster of oligopeptide permease (opp) genes, which has been shown to have great importance […]


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GIPSy in publications

 (6)
PMCID: 5406005
PMID: 28445543
DOI: 10.1371/journal.pone.0176347

[…] against the uniprot database []. the genome with the corrected sequences, which included the fixed frameshifts, was then re-annotated using rasttk., 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) […]

PMCID: 5383145
PMID: 28384209
DOI: 10.1371/journal.pone.0175116

[…] other species. phage 5, predicted as incomplete in the reference genome, was absent in l. lactis io-1, l. cremoris kw2, l. cremoris uc5099 and partially present in both l. garvieae strains., in the gipsy predictions, we identified 9 genomic islands (geis), 5 metabolic islands (mis), 4 symbiotic islands (sis) and 3 miscellaneous islands (msis), which were predicted as harboring both metabolic […]

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

[…] the versions described in this paper are versions mcoc01000000, mcob01000000, mcoa01000000, mcnz01000000, mcny01000000, mcnx01000000, and mcnw01000000., 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 […]

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

[…] []. 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 […]

PMCID: 4988695
PMID: 27532207
DOI: 10.1371/journal.pone.0161032

[…] chromosomal deviations in gc content, known as genomic islands (geis) (http://www.pathogenomics.sfu.ca/islandviewer/) []. additionally, the newly developed genomic island prediction software (gipsy) [] was utilized to evaluate the presence of different classes of geis in strain m213., venn diagrams, phylogenetic comparisons, core genome, pan genome, synteny plots and other comparative […]


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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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