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Open Access Research article

The mosaicism of plasmids revealed by atypical genes detection and analysis

Emanuele Bosi, Renato Fani and Marco Fondi*

Author Affiliations

Lab. of Microbial and Molecular Evolution, Dept. of Evolutionary Biology, Via Romana 17-19, University of Florence, Italy

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BMC Genomics 2011, 12:403  doi:10.1186/1471-2164-12-403

Published: 8 August 2011

Additional files

Additional file 1:

analyzed plasmds dataset. Table with the information concerning the 1853 analyzed plasmids, including their name, their accession number and PAGs content at different CI thresholds.

Format: XLSX Size: 211KB Download file

Open Data

Additional file 2:

all PAGs sequences. Fasta files embedding all the sequences identified as PAGs at the different CI values.

Format: ZIP Size: 9.8MB Download file

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Additional file 3:

lower confidence PAGs distribution. PAGs (retrieved at 70%, 80% and 90% CIs) ditribution across the plasmids composing the dataset.

Format: PPT Size: 173KB Download file

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Open Data

Additional file 4:

PAGs and taxonomy. Full taxonomical distribution of PAGs.

Format: PPT Size: 953KB Download file

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Additional file 5:

lower confidence PAGs and plasmids size for lower CI values. Scatterplots illustrating the low positive correlation existing between plasmids size and their PAGs content, with three different PAGs datasets retrieved at a) 70%, b) 80% and c) 90%.

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Additional file 6:

lower confidence PAGs functional annotation. a) Full COG http://www.ncbi.nih.gov/COG webcite functional annotation of PAGs retrieved at 70%, 80% and 90% Cis. In particular, the function each of the sequences embedded in these datasets was inferred according to the one assigned to the best BLAST hit of COG database. b) Full Blast2GO functional annotation of PAGs retrieved at 95% CI.

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Additional file 7:

lower confidence PAGs length. The length of lower confidence PAGs encoded proteins.

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Additional file 8:

clusters of lower confidence PAGs. Results of gene clusters analysis for a) 100, 200 and 300 bp gene distance threshold and b) for PAGs retrieved at 70%, 80% and 90% CIs.

Format: PPT Size: 182KB Download file

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Additional file 9:

complete PAGs clusters accession codes. The complete list of all identified PAGs (retrieved at 95% CI threshold) clusters (at 200 bp threshold), together with their corresponding organisms and GI codes.

Format: XLS Size: 106KB Download file

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Additional file 10:

the atypical mer, tet, maxi and cbi clusters. Schematic representation of the atypical mer, tet, maxi and cbi clusters found in different plasmids of different microorganisms.

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Additional file 11:

lower confidence PAGs in CMPs and NCMPs. Distribution of lower confidence PAGs among CMPs and NCMPs

Format: PPT Size: 95KB Download file

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Additional file 12:

PAGs clusters in CMPs and NCMPs. Distribution and length of PAGs clusters in CMPs and NCMPs.

Format: PPT Size: 178KB Download file

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