PSCAN

Scans proteins using PRINTS

PRINTS is a database of diagnostic protein signatures, or fingerprints.

Fingerprints are groups of conserved motifs or elements that togetherform a diagnostic signature for particular protein families.

An uncharacterised sequence matching all motifs or elements can then bereadily diagnosed as a true match to a particular family fingerprint.

They can be used to diagnose family relationships in newly-determinedsequences (especially from genome projects).

Usually the motifs or elements do not overlap, but are separated along asequence, though they may be contiguous in 3D-space. Fingerprints canencode protein folds and functionalities more flexibly and powerfullythan can single motifs, full diagnostic potency deriving from the mutualcontext provided by motif neighbours.

Diagnostically, this is more powerful than using single motifs by virtueof the biological context afforded by matching motif neighbours.

pscan finds matches between a query protein sequence and the motifs orelements in the PRINTS database. It reports various classes of matches:

• Matches where all elements of a motif exist in the correct order
• Matches where all elements exist but some are in the incorrect order
• Matches where some elements match and are in the correct order
• Miscellaneous matches.

The home web page of the PRINTS database is:http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/

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