The Alignment Viewer displays multiple alignments (in Clustal, MSF and Modeller format) to reveal the sequence conservation among homologous proteins. This way, it is possible to understand the variability of important protein regions on the sequence level and to schematically visualize the position of the alignments with respect to each other. In addition, protein regions or the complete set of sequences may be selected for the generation of customized protein profiles.

fig. 1

Schematic view of a master-slave alignment which was generated by selecting a group of homologues hits (from a fold recognition search, ProFit) in the Hit Viewer. The colored horizontal bars indicate conserved Prosite patterns.

fig. 2

Sequence view of a master-slave alignment colored by a predefined color scheme (here, chemical properties of amino acids).