This Web tool displays for each found motif (profile/pattern/rule) hit within a protein sequence: the hit sequence, score (for hits against a profile), PROSITE description and link. In addition, if predicted; biological features associated with hit sequences (see bellow for details) are also indicated.

Results are separated into different types: hits by PROSITE 'profiles', 'profiles with a high probability of occurrence', 'patterns', 'patterns with a high probability of occurrence or by user-defined patterns'. Inside each of these categories, hits by protein are sorted by their N-ter position but multiple hits against a similar motif are grouped together.

In addition for each matched protein, a graphical view in form of a downloadable png (Portable Network Graphics) image represents all its matches (of the aforementioned type) and detected features. Profile hits are represented as colored shapes with their PROSITE name; Pattern hits are shown (separated) as thin colored bars without text. If a match overlaps with the previous one, it will be shown on a different line or if overlap size is smaller than 10% of the match size, the match will be shown on the same line, its overlapping start will be truncated and replaced by a vertical red bar (showing that there is a small overlap).

Biological features

For certain profiles, additional biologically meaningful information about residues inside matches is defined. This additional information comes from the mapping of biologically meaningful residues to PROSITE profiles. It is used to make functional/structural predictions of profile matches more accurate (as profiles show enhanced sensitivity over patterns, but because of their relaxed stringency loose functional/structural discriminativity).

If certain conditions expected for the functional and/or structural properties associated with the domain are fulfilled the properties are shown as 'Predicted features'. For each feature, the Swiss-Prot feature key, the position/range, the feature description (if any), and the condition that triggered the detection are shown.

Conditions can be specific amino acid inside hit, group of sub-conditions in which all conditions must be true in order for the group condition to be true, case between different sub-conditions/groups etc...

Features associated with conditions that were not fulfilled are shown as 'Absent features' in the same way as for predicted ones except that condition here shows why the feature has not been detected (condition/case not true and/or incomplete group).

On the graphical view, features are shown on top of hits; depending on their type as bridges, horizontal 'bars', vertical pins.

Individual view

If several proteins are matched; next to each graphical view an 'individual view' link is shown. It will link to a page displaying only the hits for that particular protein.

Match/sequence highlighting

When hits for only one protein are shown, and if you have a Mozilla based web browser (Mozilla, FireBird/Fox, Netscape 7) you'll be able to see feature residues highlighted (green for predicted features, gray for absent features) on both the match and the full protein sequence (if shown) when you move your mouse cursor over a feature line. In addition if the full sequence of the protein is shown (only sequences of proteins entered under 'Protein(s) to be scanned' in ScanProsite are shown, the full sequences of matching proteins found in protein databases are not), the match region in the protein sequence will be highlighted in yellow when you move your mouse cursor over that match in the graphical view or the text view.

Highlights are persistent as long as you don't move your cursor over another match/feature (note that left/right margins are immune to cursor moves).