TMCompare is an alignment and visualization tool for comparison of sequence information for membrane proteins contained in SWISS-PROT entries, with structural information contained in PDB files. The program can be used for: detection of breaks in alpha helical structure of transmembrane regions, examination of differences in coverage between PDB and SWISS-PROT files, examination of annotation differences between PDB files and associated SWISS-PROT files, examination and comparison of assigned PDB alpha helix regions and assigned SWISS-PROT transmembrane regions in linear sequence (one letter code) format, examination of these differences in 3D using the CHIME plugin, allowing, analysis of the alpha and non-alpha content of transmembrane regions.