Improved genomic island predictions with IslandPath-DIMOB

Abstract

Motivation: Genomic islands (GIs) are clusters of genes of probable horizontal origin that play a major role in bacterial and archaeal genome evolution and microbial adaptability. They are of high medical and industrial interest, due to their enrichment in virulence factors, some antimicrobial resistance genes and adaptive metabolic pathways. The development of more sensitive but precise prediction tools, using either sequence composition-based methods or comparative genomics, is needed as large-scale analyses of microbial genomes increase.

Results: IslandPath-DIMOB, a leading GI prediction tool in the IslandViewer webserver, has now been significantly improved by modifying both the decision algorithm to determine sequence composition biases, and the underlying database of HMM profiles for associated mobility genes. The accuracy of IslandPath-DIMOB and other major software has been assessed using a reference GI dataset predicted by comparative genomics, plus a manually curated dataset from literature review. Compared to the previous version (v0.2.0), this IslandPath-DIMOB v1.0.0 achieves 11.7% and 5.3% increase in recall and precision, respectively. IslandPath-DIMOB has the highest Matthews correlation coefficient among individual prediction methods tested, combining one of the highest recall measures (46.9%) at high precision (87.4%). The only method with higher recall had notably lower precision (55.1%). This new IslandPath-DIMOB v1.0.0 will facilitate more accurate studies of GIs, including their key roles in microbial adaptability of medical, environmental and industrial interest.

Availability and implementation: IslandPath-DIMOB v1.0.0 is freely available through the IslandViewer webserver {{http://www.pathogenomics.sfu.ca/islandviewer/}} and as standalone software {{https://github.com/brinkmanlab/islandpath/}} under the GNU-GPLv3.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

GI prediction accuracy of IslandPath-DIMOB and other individual methods compared with IslandViewer 4 composite method, based on the C-dataset (comparative genomics-based dataset). Prediction accuracy on the dataset of GIs identified by the comparative genomics approach IslandPick in 104 genomes. The boxplot shows the median, and the first and third quartiles as the lower and upper hinges. Outliers are indicated as black dots, if they exceed 1.5 times the interquartile range. IslandViewer 4 is a composite method, combining IslandPath-DIMOB, SIGI-HMM and IslandPick, whereas other tools are individual methods