PanFunPro: PAN-genome analysis based on FUNctional PROfiles

PanFunPro is a tool for pan-genome analysis that integrates functional domains from three Hidden Markov Models (HMM) collections, and uses this information to group homologous proteins into families based on functional domain content. We use PanFunPro to compare a set of Lactobacillus and Streptococcus genomes. The example demonstrates that this method can provide analysis of differences and similarities in protein content within user-defined sets of genomes. PanFunPro can find various applications in a comparative genomic study, starting with the basic comparison of newly sequenced isolates to already existing strains, and an estimation of shared and specific genomic content. Furthermore, it can potentially be used in the determination of target sequences for in silico bacterial identification, as well as for epidemiological studies.