IslandPath protocols

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IslandPath specifications

Information


Unique identifier OMICS_08269
Name IslandPath
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Publication for IslandPath

IslandPath in pipelines

 (2)
2017
PMCID: 5522923
PMID: 28729256
DOI: 10.1128/genomeA.00496-17

[…] is 85.68% with an average gene length of 721 bp. there are 49 interspersed nuclear elements and 111 tandem repeats, including 1 microsatellite dna and 100 minisatellite dnas in the genome. the islandpath-diomb () program was used to predict the genomics islands, phast () was for the prophage prediction, and crisprfinder () for clustered regularly interspaced short palindromic repeat […]

2016
PMCID: 4888996
PMID: 27198035
DOI: 10.1128/genomeA.01764-15

[…] ncbinr, cog, go, kegg, swiss-prot, and trembl. trnascan (), rnammer (), and rfam () were used to predict trnas, rrnas, and small rnas, respectively. gene islands and prophages were predicted using islandpath-diomb () and phast software ()., the genome size of e. pernyi is 3.09 mb with a g+c content of 38.35%. a total of 626 mb of clean data were generated, reaching a genome coverage depth […]


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IslandPath in publications

 (19)
PMCID: 5940136
PMID: 29602809
DOI: 10.1534/g3.118.200018

[…] predicted by the ncbi prokaryotic genome annotation pipeline on the genbank database. genomic islands, insertion sequences, interspersed repetitive sequences, and tandem repeats were predicted with islandpath-diomb program (), isfinder (https://www-is.biotoul.fr/), repeatmasker v4.0.5 (), and trf v4.0.7b () with default parameters, respectively., functional annotations were conducted by blastp […]

PMCID: 5742357
PMID: 29326683
DOI: 10.3389/fmicb.2017.02578

[…] webserver based program, islandviewer 4 (; ) was used to identify and visualize the putative genomic islands in the genome of m. yongonense dsm 45126t with three prediction methods: islandpick (), islandpath () and sigi-hmm (). among the selected putative regions, orfs with high sequence similarities to other genus in the genome of m. yongonense dms 45126t (m. yongonense type i) were selected […]

PMCID: 4997845
PMID: 27324770
DOI: 10.1128/AAC.00236-16

[…] server () using as input the annotation generated by rast. briefly, islandviewer uses two algorithms to predict genomic islands; both of them are based on sequence composition methods (sigi-hmm and islandpath/dimob). sigi-hmm incorporates synonymous codon usage as the statistical feature. different species have different preferences for synonymous codon usage; the frequencies at which codons […]

PMCID: 4887561
PMID: 27293536
DOI: 10.1016/j.csbj.2016.05.001

[…] analysis. both methods use a sliding window to scan the genome, and sequences or genes inside each window are used for computation., other methods use only a single discrimination criterion, such as islandpath-dinuc , and sigi-hmm . islandpath-dinuc uses a single-threshold method to predict gis as multiple consecutive genes with only dinucleotide bias. sigi-hmm predicts gis and putative donor […]

PMCID: 4519734
PMID: 26223387
DOI: 10.1038/srep12561

[…] of bacteria and 519 essential genes of archaeon from the deg database, the proportions of essential genes in and out of gis can be studied, respectively. the statistical result is displayed in . islandpath-domb, which is defined as a more strict and more precise method, is based on sequence composition method, both dinucleotide bias and the presence of one or more mobility genes in the genes […]


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IslandPath institution(s)
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada

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