Phydbac (phylogenomic display of bacterial genes) implemented a method of 
phylogenomic profiling using a distance measure based on normalized BLAST 
scores. This method was able to increase the predictive power of phylogenomic 
profiling by about 25% when compared to the classical approach based on Hamming 
distances. Here we present a major extension of Phydbac (named here Phydbac2), 
that extends both the concept and the functionality of the original web-service. 
While phylogenomic profiles remain the central focus of Phydbac2, it now 
integrates chromosomal proximity and gene fusion analyses as two additional 
non-similarity-based indicators for inferring pairwise gene functional 
relationships. Moreover, all presently available (January 2004) fully sequenced 
bacterial genomes and those of three lower eukaryotes are now included in the 
profiling process, thus increasing the initial number of reference genomes (71 
in Phydbac) to 150 in Phydbac2. Using the KEGG metabolic pathway database as a 
benchmark, we show that the predictive power of Phydbac2 is improved by 27% over 
the previous version. This gain is accounted for on one hand, by the increased 
number of reference genomes (11%) and on the other hand, as a result of 
including chromosomal proximity into the distance measure (16%). The expanded 
functionality of Phydbac2 now allows the user to query more than 50 different 
genomes, including at least one member of each major bacterial group, most major 
pathogens and potential bio-terrorism agents. The search for co-evolving genes 
based on consensus profiles from multiple organisms, the display of Phydbac2 
profiles side by side with COG information, the inclusion of KEGG metabolic 
pathway maps the production of chromosomal proximity maps, and the possibility 
of collecting and processing results from different Phydbac queries in a common 
shopping cart are the main new features of Phydbac2. The Phydbac2 web server is 
available at http://igs-server.cnrs-mrs.fr/phydbac/.