We present a plug-in for Pathway Tools, an integrated systems biology software to create, maintain and query Pathway/Genome Databases. Fully integrated into the graphical user interface and menu, this plug-in extends the applications functionality by the ability to create multiple sequence alignments, systematically annotate insertion sequence (IS) elements and analyse their activity by cross-species comparison tools. Microarray probes can be automatically mapped to target genes, and expression data obtained with these arrays can be transformed into input formats needed to visualize them in the various omics viewers of Pathway Tools. The plug-in API itself allows developers to integrate their own functions into the Pathway Tools menu.