For the evaluation of the MDS-based visualizations we analyzed the microbial genomes of Escherichia coli K-12, Bacillus subtilis, Vibrio cholerae and Thermus thermophilus HB8. We used annotated DNA sequence data in the EMBL format publicly available from EBI [23]. Ribosomal protein genes were extracted from the datasets of the completely annotated genomes. Putative alien genes were selected according to the following information: On chromosome 1 of V. cholerae two genomic islands were predicted by SIGI-HMM that comprise a gene cluster for a toxin-coregulated pilus and fragments of a temperate filamentous phage described in [24]. Both clusters are closely associated with the pathogenicity of V. cholerae. For Bacillus subtilis 10 integrated prophages have been described based on experimental evidence and theoretical considerations [25-28]. Nine of these prophages overlap with genomic islands as predicted by SIGI-HMM. For Escherichia coli K-12 the authors of [29] used different compositional variables and estimated that about 18% of the genome have been imported by horizontal gene transfer. In contrast, SIGI-HMM predicted 580 genes (13,6%) to be putatively alien. The largest genomic islands comprise the cryptic prophages CP4-6, DLP12, e14, Rac, Qin, CP4-44, CPS-53, Eut, CP4-57, and the phage-like element KpLE2 (reviewed in [30]). For the extremophilic bacterium Thermus thermophilus HB8 no genomic islands have been described so far. SIGI-HMM predicted a contiguous gene cluster of 5 genes associated with functions in cell wall biosynthesis to be putative alien. The total number of putative alien genes and the number of ribosomal protein genes for all species considered here are summarized in table 1. Additional file 1 provides a detailed list of all putative alien genes used for the visualization.