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Protocols

COLOMBO/SIGI-HMM specifications

Information


Unique identifier OMICS_08273
Name COLOMBO/SIGI-HMM
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Perl
Computer skills Medium
Stability Stable
Maintained Yes

Subtools


  • FSIGI-HMM
  • SIGI
  • SIGI-HMM

Versioning


No version available

Publications for COLOMBO/SIGI-HMM

COLOMBO/SIGI-HMM citations

 (113)
library_books

Background Adjusted Alignment Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer

2018
Front Microbiol
PMCID: 5911508
PMID: 29713314
DOI: 10.3389/fmicb.2018.00711

[…] on this data set and the resulting figures are shown in figure . it is clear from the figure that cvt(3), d2*(3,1) and d2*(4,1) perform much better than the other methods. in langille et al. (), sigi-hmm and islandpath/dimob showed the highest accuracy of 0.86. we did not include them in our comparison because they incorporate other information such as codon uasge, dinucleotide bias, gene […]

library_books

Pan Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation

2018
Front Microbiol
PMCID: 5880901
PMID: 29636744
DOI: 10.3389/fmicb.2018.00577

[…] and classified using the isfinder platform (). a developed islandviewer 3 (), which integrates two sequence composition genomic islands (gis) prediction method, i.e., islandpath-dimob () and sigi-hmm (), and a comparative genomic gis prediction method islandpick (), was applied for the computational identification of putative gis. in addition, crispr (clustered regularly interspaced […]

library_books

Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single Molecule Real Time sequencing

2018
Sci Rep
PMCID: 5854607
PMID: 29545612
DOI: 10.1038/s41598-018-23053-7

[…] the genome was analyzed for the presence of cripsrs using the cirsprfinder web tool. genomic islands were inferred using islandviewer 3, which integrates results of three prediction methods: sigi-hmm, islandpath-dimob and islandpick., average nucleotide identities (ani) were calculated using the orthoani method. whole-genome alignments were generated using nucmer 3.1 (mummer 3.23). best […]

library_books

Comparative Genomics and Identification of an Enterotoxin Bearing Pathogenicity Island, SEPI 1/SECI 1, in Staphylococcus epidermidis Pathogenic Strains

2018
Toxins
PMCID: 5869381
PMID: 29495323
DOI: 10.3390/toxins10030093

[…] were successively analyzed using the uniprot database., mges were explored as previously described []. pathogenicity islands were identified using islandviewer 4 [], which associates islandpick, sigi-hmm, and islandpath-dimob for the identification of pathogenicity islands. this tool displays the results as circular graphical images and allows localization of the putative pathogenicity […]

library_books

Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios

2018
BMC Genomics
PMCID: 5809883
PMID: 29433445
DOI: 10.1186/s12864-018-4531-2

[…] the genes acquired or lost during the evolutionary process of the genus vibrio were categorized based on searching against the cog database (http://www.ncbi.nih.gov/cog/) using rps-blast program. sigi-hmm [] was used to infer whether genes in the genomes were acquired through hgt., ani between any two genomes of the small dataset was calculated using a custom perl script adapted from ani.pl […]

library_books

Genome analysis of Mycoplasma synoviae strain MS H, the most common M. synoviae strain with a worldwide distribution

2018
BMC Genomics
PMCID: 5797395
PMID: 29394882
DOI: 10.1186/s12864-018-4501-8

[…] geneious alignment tool with the default parameters. the search for pathogenicity genomic islands was conducted using the islandviewer3 server (http://www.pathogenomics.sfu.ca/islandviewer) and the sigi-hmm and islandpath-dimob methods []. the phage search tool (phast) (http://phast.wishartlab.com) was used to detect complete and/or incomplete prophage sequences []. clustered regularly […]


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COLOMBO/SIGI-HMM institution(s)
Institut für Informatik, Universität Göttingen, Göttingen, Germany

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