IslandPath statistics

info info

Citations per year

info

Popular tool citations

chevron_left Genomic island prediction chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

Protocols

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 citations

 (21)
library_books

Genome Wide Analysis of Mycoplasma bovirhinis GS01 Reveals Potential Virulence Factors and Phylogenetic Relationships

2018
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 […]

library_books

Role of the DNA Mismatch Repair Gene MutS4 in Driving the Evolution of Mycobacterium yongonense Type I via Homologous Recombination

2017
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 […]

call_split

Complete Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain zly1309F, Isolated from Endangered Tibetan Antelope

2017
PMCID: 5522923
PMID: 28729256
DOI: 10.1128/genomeA.00496-17
call_split See protocol

[…] 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 […]

library_books

Isolation and Characterization of NDM Positive Escherichia coli from Municipal Wastewater in Jeddah, Saudi Arabia

2016
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 […]

call_split

Genome Sequence of Enterococcus pernyi, a Pathogenic Bacterium for the Chinese Oak Silkworm, Antheraea pernyi

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

[…] 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 […]

library_books

Computational methods for predicting genomic islands in microbial genomes

2016
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 […]


Want to access the full list of citations?
IslandPath institution(s)
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada

IslandPath reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review IslandPath