Academic
Publications
Detecting genomic islands using bioinformatics approaches

Detecting genomic islands using bioinformatics approaches,10.1038/nrmicro2350,Nature Reviews Microbiology,Morgan G. I. Langille,William W. L. Hsiao,Fi

Detecting genomic islands using bioinformatics approaches   (Citations: 7)
BibTex | RIS | RefWorks Download
Bacterial genomes contain clusters of genes that are acquired by horizontal transfer, called genomic islands (GIs). GIs are frequently associated with microbial adaptations that are of medical and environmental interest, and they have had a substantial impact on bacterial evolution. Therefore, there is growing interest in efficiently identifying GIs in newly sequenced bacterial genomes. Several computational methods for detecting GIs have been developed recently, presenting researchers with a myriad of choices. Here, we discuss the limitations and benefits of the main approaches that are available and present guidelines to aid researchers in effectively identifying these important genomic regions.
Journal: Nature Reviews Microbiology - NAT REV MICROBIOL , vol. 8, no. 5, pp. 373-382, 2010
Cumulative Annual
View Publication
The following links allow you to view full publications. These links are maintained by other sources not affiliated with Microsoft Academic Search.
    • ...). Five RDs (RD1, RD4, RD29, RD32, and RD45) were found to contain prophage remnants, indicating that they have been acquired in the reference genome by horizontal transfer. We analyzed the RDs for structural features of genomic islands (GIs) including sequence composition bias, tRNA genes as insertion site, direct repeats flanking the RD and integrases ...

    Xiao Zhenget al. Identification of Genes and Genomic Islands Correlated with High Patho...

    • ...Both vcrA and bvcA have a highly unusual, low %(G+C) codon bias that appears maladapted to Dehalococcoides genomes [20], and both are found within a low %(G+C) “genomic island” (GI) [21] that interrupts local gene synteny relative to other Dehalococcoides strains...
    • ...These findings are consistent with ssrAspecific integration described for other bacteria [21,24], as well as a class of integrating and mobilizing elements that encode their own specific integration but do not replicate independently from the chromosome nor encode for conjugation [33]...

    Paul J McMurdieet al. Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a ...

    • ...Two major problems with these methods are that false predictions can occur due to natural variation in the genome (sometimes due to highly expressed genes) and that horizontally transferred DNA will ameliorate (change to the host genome) over time; therefore, limiting predictions to only recently acquired GIs [8]...

    Ren-Feng Liet al. Genomic Islands Analysis of Three Actinobacillus pleuropneumoniae Stra...

    • ...Methods based on genomic comparison, detection of composition bias and search of mobility genes are the most performing tools for the flexible genome characterization [45]...

    Jean-Claude Ogieret al. Units of plasticity in bacterial genomes: new insight from the compara...

Sort by: