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Table 1 Comparison of the GIs of eight marine bacteria referred to as Control Genomes where GIs were available in previous studies and the GIs predicted by this study for the same genomes by IslandViewer

From: Patterns and architecture of genomic islands in marine bacteria

Bacterial strain Previous studies GIs IslandViewer GIs Comparison analyses (Previous vs. IslandViewer GIs)
Number of GIs Total GIs length detected in control genomes (kb) #GIs present (+) Extra GIsb(+) #GIs absent (−) Total GIs length with IslandViewer prediction (kb)* (% overlap)a(kb) Recallb(sensitivity)(%) Precisionc(%)
P. marinus str. MIT93121 5 233 3d 0 3 44.9 19.3 50 100
S. sp. RCC3072 15 271 9 1 6 56.9 18.7 60 90
S. sp. WH78032 11 344 3 2 8 73.7 20.3 27 60
S. sp. CC96052 20 505.3 18 4 2 300.4 54.3 90 82
S. sp. CC93112 24 578.6 9 2 15 125.9 16.9 38 82
A. macleodii “deep ecotype”3 13 480 6 5 7 272.7 69.6 46 55
S. ruber DSM138554 3 221.8 3 1 0 168.2 41.1 100 75
S. ruber M84 2 265.9 2 3 0 144.9 44.5 100 40
Average        35.58 64 73
  1. 1Coleman et al., 2006. Method used to detect GIs: Comparative genomics using 2 Prochlorococcus marinus genomes.
  2. 2Dufresne et al., 2008. Method used to detect GIs in Synechococcus genomes: Modified protocols published by Hsiao[15] and Rusch et al.[36] specifically deviations of tetranucleotide frequency, presence of MGE, tRNAs and the occurrence of core genome gene blocks.
  3. 3Ivars-Martínez et al., 2008. Method used to detect GIs: Comparative genomics using 2 Alteromonas macleodii strains genomes.
  4. 4Peña et al., 2010. Method used to detect GIs: Comparative genomics using 2 Salinibacter ruber genomes.
  5. a)% overlap between GIs of previous studies and this study.
  6. b) Recall (sensitivity): GIs present (+)/ [GIs present (+) plus GIs absent (−)].
  7. c) Precision: GIs present (+)/[GIs present (+) plus Extra GIs (+)].
  8. d) Two of these three GIs detected by IslandViewer match different sections of the biggest GI of Prochlorococcus marinus str. MIT9312 (see in Figure1).
  9. * All GIs detected by IslandViewer/IslandPick included some small genomic islets (<9.5 kb) that are not included in Additional file3: Table S3.