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Open Access Highly Accessed Research article

A quantitative account of genomic island acquisitions in prokaryotes

Tom E Roos12 and Mark WJ van Passel3*

Author Affiliations

1 Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands

2 Netherlands Bioinformatics Centre, Nijmegen, The Netherlands

3 Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands

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BMC Genomics 2011, 12:427  doi:10.1186/1471-2164-12-427

Published: 24 August 2011

Additional files

Additional file 1:

Example of a GI clustering conflict in Clostridium botulinum Ba4 657. Example of a GI clustering conflict. In Clostridium botulinum Ba4 657, six GIs larger than 10 kb are identified by IslandViewer. The CI-25 threshold sequence has a genomic dissimilarity to its genome of 30,86. GI-1 and GI-5 are compositionally more similar to each other (δ* of 22,7), as are GI-2 and GI-5 (δ* of 27,7). However, GI-1 and GI-2 are much more dissimilar (δ* of 42,1), and therefore could be considered as a clustering conflict.

Format: DOCX Size: 78KB Download file

Open Data

Additional file 2:

Complete table for all genomes that contain GIs. Complete table for all genomes (> 800 kb) that contain GIs ( > 10 kb), and have no conflicts in the genome. In green are highlighted the cases where clusters of three GIs are found. The dissimilarity cut-off is expressed in the genomic dissimilarity value between the Core Island (in this case, CI-10) and the genome sequence.

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Open Data

Additional file 3:

List of genomes with clustered GIs. List of genomes with clusters in which more than 1 GI are located, using the compositional threshold of CI-10.

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Additional file 4:

Clustered GIs in multichromosomal genomes. Clusters of GIs in genomes with multiple chromosomes using cut-off of CI-10. Highlighted in green are clustered GIs that are located on a different replicon.

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Open Data

Additional file 5:

Characteristics of all Genomic Islands in this study. Characteristics of all Genomic Islands (5447) analyzed in this study, including their number in the genome of occurrence. The 1787 GIs that comply with the criteria (Genome > 800 kb, GI size > 10 kb, no conflicts in the clustering analysis and using cut-off threshold CI-10) are separated from the rest of the GIs by a blank line.

Format: XLSX Size: 720KB Download file

Open Data