Bosi et al. BMC Genomics 2011, 12:403 http://www.biomedcentral.com/1471-2164/12/403 most are involved in the overall process of DNA mobili- zation, although other biologically relevant functions have been identified, such as transcription, pathogenesis and antibiotic resistance. The fact that we have retrieved the genes encoding for these functions associated to aty- pical DNA regions has important biological drawbacks, underlining the important role of HGT in the bacterial sharing of these key traits. Importantly PAGs are often found in multi-cistronic clusters embedding two or more genes. However, the fact that shorter plasmids (embedding 2 or 3 genes) are much more frequent than longer ones, probably indicates that PAGs clusters are fragmented following thier integration or that, alterna- tively, the transfer of shorter clusters is favoured in respect to longer gene arrays. Finally, our analysis revealed that most of the PAGs might be of plasmid origin suggesting that plasmid-plas- mid gene exchange might be favoured in respect to phage-plasmid and chromosome-plasmid ones. This is in partial agreement with previous findings [40] and reveals that a sort of preferential gene flow between vehicles of the same type (in our case plasmids) might exist. Additional material 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. Additional file 2: all PAGs sequences. Fasta files embedding all the sequences identified as PAGs at the different CI values. Additional file 3: lower confidence PAGs distribution. PAGs (retrieved at 70%, 80% and 90% CIs) ditribution across the plasmids composing the dataset. Additional file 4: PAGs and taxonomy. Full taxonomical distribution of PAGs. 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%. Additional file 6: lower confidence PAGs functional annotation. a) Full COG http://www.ncbi.nih.gov/COG 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. Additional file 7: lower confidence PAGs length. The length of lower confidence PAGs encoded proteins. 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. 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. 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. Page 11 of 12 Additional file 11: lower confidence PAGs in CMPs and NCMPs. Distribution of lower confidence PAGs among CMPs and NCMPs Additional file 12: PAGs clusters in CMPs and NCMPs. Distribution and length of PAGs clusters in CMPs and NCMPs. Acknowledgements and Funding MF is supported by a postdoctoral fellowship from “Fondazione Adriano Buzzati-Traverso”. We are grateful to three anonymous reviewers for their useful comments and suggestions that greatly improved the manuscript. Authors’ contributions MF conceived of the study and wrote the Perl codes for the analyses. 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