The Hit Viewer displays search or comparison results in a tabular format. The results from sequence-to-sequence searches (Blast), sequence-to-structure searches (ProFit), and structure-to-structure searches (ProSup) are presented in a table, similar to a spreadsheet. The Hit Viewer is a tool to organize tables of this type and allows to send alignments of hits for display to the Alignment Viewer and Structure Viewer, or to tweak single alignments by re-submitting them to sequence- and structure-based algorithms.

The Hit Viewer simplifies the interpretation of hit lists considerably by coloring hits according to family relationships with respect to a selected classification scheme. Furthermore, it provides the researcher with essential information like domain composition, domain borders, structure similarity, sequence similarity, function similarity and function-specific patterns.

Result of a structure-to-structure search (ProSup), ordered by equivalent residues. Hits with identical colors belong to the same structure family. The info window displays the classification of the first hit (according to SCOP).