COLOMBO/SIGI-HMM protocols

COLOMBO/SIGI-HMM statistics

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Associated diseases

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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

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Publications for COLOMBO/SIGI-HMM

COLOMBO/SIGI-HMM in pipelines

 (5)
2016
PMCID: 4886054
PMID: 27303384
DOI: 10.3389/fmicb.2016.00797

[…] (juhas et al., ; bustamante et al., ; acuña et al., )., the three regions are enriched in horizontally transferred genes (alien genes) based on the predictions obtained from the application of sigi-hmm (figure ). putative genomic island 1 (figure : gi-1, 42–126 kbp) is ~85 kbp in size and has an average g+c-content of 56.1%, which is 11% higher than the average g+c-content of the complete […]

2015
PMCID: 4667477
PMID: 26626322
DOI: 10.1186/s12864-015-2216-7

[…] contains 140 pseudogenes in total, representing around 6.8 % of the total gene number, thus significantly higher than the 1–5 % average figure reported for other bacterial genomes []. the colombo sigi-hmm software [] predicts 1.5 % of the total gene content of strain atcc 53608 to originate from hgt (fig. ). the genome of atcc 53608 was found to be moderately repetitive, containing 15 […]

2013
PMCID: 3593330
PMID: 23516232
DOI: 10.1128/genomeA.00218-12

[…] classic secretion systems in the gram-negative bacteria were not identified, which has been reported in other virulent r. anatipestifer strains. moreover, three genomic islands were identified using sigi-hmm; these were 4,772 bp, 3,537 bp, and 8,289 bp., overall, the genome sequence of avirulent r. anatipestifer ra-sg will provide the basis for a better understanding of the molecular […]

2012
PMCID: 3401170
PMID: 22911766
DOI: 10.1371/journal.pone.0041247

[…] replicons were identified by pcr and sequencing are marked with c (which could indicate the presence of both an inci1 and an incfib plasmids or the presence of a cointegrated plasmid)., we used sigi-hmm and comparative genomic analyses with the mauve algorithm and rast – to predict and identify putative genomic islands among the 16 genomes analyzed here. as expected, a number of putative […]

2009
PMCID: 2702500
PMID: 19187283
DOI: 10.1111/j.1462-2920.2008.01825.x

[…] have been developed on the basis of a compilation of all known ecf σ-factors (). putative genomic islands, referred to as alien genes and/or highly expressed cds, were searched with a score-based fsigi-hmm program (; )., repeated elements within the genomic sequence were calculated and analysed using the programs repfind and repvis, which both are part of the reputer software package (). […]


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COLOMBO/SIGI-HMM in publications

 (111)
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 […]

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 […]

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 […]

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 […]

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 […]


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

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