XFINGER - A TOOL FOR SEARCHING AND VISUALIZING PROTEIN FINGERPRINTS AND PATTERNS

A tool for searching pattern and fingerprint databases is described. F ingerprints are groups of motifs excised from conserved regions of seq uence alignments and used for iterative database scanning. The constit uent motifs ave thus encoded as small alignments in which sequence inf ormation is maximised with each database pass; they therefore differ f rom regular-expression patterns, in which alignments ave reduced to si ngle consensus sequences. Different database formats have evolved to s tove these disparate types of information, namely the PROSITE dictiona ry of patterns and the PRINTS fingerprint database, but programs have not been available with the flexibility to search them both. We have d eveloped a facility to do this: the system allows query sequences to b e scanned against either PROSITE, the full PRINTS database, or against individual fingerprints. The results of fingerprint searches ave disp layed simultaneously in both text and graphical windows to vender them move tangible to the user. Where structural coordinates are available , identified motifs may be visualised in a 3D context. The program run s on Silicon Graphics machines using GL graphics libraries and on mach ines with X servers supporting the PEX extension: its use is illustrat ed here by depicting the location of low-density lipoprotein-binding ( LDL) motifs and leucine-rich repeats in a mosaic G-protein-coupled rec eptor (GPCR).