Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Research article

Short and long-term genome stability analysis of prokaryotic genomes

Matteo Brilli124*, Pietro Liò3, Vincent Lacroix2 and Marie-France Sagot12

Author Affiliations

1 INRIA, Grenoble Rhône-Alpes, Lyon, France

2 Laboratoire de Biométrie et Biologie Évolutive, Universitè Lyon 1 UMR CNRS 5558, Lyon, France

3 Computer Laboratory, University of Cambridge, 15 JJ Thompson Avenue, Cambridge, CB3 0FD, UK

4 Present address: Fondazione Edmund Mach/CRI - Functional genomics - Via Mach 1, 38010 San Michele all’Adige, Trento, Italy

For all author emails, please log on.

BMC Genomics 2013, 14:309  doi:10.1186/1471-2164-14-309

Published: 8 May 2013

Additional files

Additional file 1:

The Genus dataset.The genus dataset allowed to increase the number of comparisons for parameter identification.

Format: PDF Size: 37KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Cyanobacteria. Comparisons within the P. marinus species and of members of two other cyanobacterial genera: Synechococcus (×) and Cyanothece (∘). The comparisons between P. marinus strains give on average larger stability values than for the other comparisons that cannot be explained by the different phylogenetic distances in the comparisons. If all these genomes were compared as a group, it would be more difficult, if not impossible, to discern the higher stability of P. marinus.

Format: PDF Size: 183KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Relationship between backbone and genome organization stability by species. The species specific relationship between GOS and BS. In the title we report the abbreviated name of the species and the regression coefficient. The size of the markers is proportional to the average phylogenetic distance within the species.

Format: PDF Size: 551KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

Relationship between genome organization stability and genomic fluidity by species. Relationship between genome organization stability (GOS) and genomic stability (σ). Plots are in double logarithmic scale.

Format: PDF Size: 861KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Distribution of singleton size by species. Distribution of the size of singleton components. Plots are in double logarithmic scale; x-axis is the length of the singleton gene clusters, y-axis is the absolute abundance.

Format: PDF Size: 385KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

Removed proteins are mostly mobile elements. Most of the proteins removed in the pre-processing step have significant similarity to proteins in the Aclame database containing mobile elements [58,59].

Format: PDF Size: 44KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data