XFINGER: A tool for searching and visualising protein fingerprints and patterns
| Autor: | Teresa K. Attwood, D. N. Perkins |
|---|---|
| Rok vydání: | 1996 |
| Předmět: |
Statistics and Probability
Databases Factual education Receptors Cell Surface Context (language use) Sequence alignment PROSITE Biology computer.software_genre Biochemistry GTP-Binding Proteins Server Consensus sequence Animals Amino Acid Sequence Graphics Molecular Biology Sequence business.industry Fingerprint (computing) Proteins Pattern recognition Computer Science Applications Lipoproteins LDL Computational Mathematics Computational Theory and Mathematics Artificial intelligence Data mining business computer Software |
| Zdroj: | Bioinformatics. 12:89-94 |
| ISSN: | 1460-2059 1367-4803 |
| Popis: | A tool for searching pattern and fingerprint databases is described. Fingerprints are groups of motifs excised from conserved regions of sequence alignments and used for iterative database scanning. The constituent motifs are thus encoded as small alignments in which sequence information is maximised with each database pass; they therefore differ from regular-expression patterns, in which alignments are reduced to single consensus sequences. Different database formats have evolved to store these disparate types of information, namely the PROSITE dictionary of patterns and the PRINTS fingerprint database, but programs have not been available with the flexibility to search them both. We have developed a facility to do this: the system allows query sequences to be scanned against either PROSITE, the full PRINTS database, or against individual fingerprints. The results of fingerprint searches are displayed simultaneously in both text and graphical windows to render them more tangible to the user. Where structural coordinates are available, identified motifs may be visualised in a 3D context. The program runs on Silicon Graphics machines using GL graphics libraries and on machines with X servers supporting the PEX extension: its use is illustrated here by depicting the location of low-density lipoprotein-binding (LDL) motifs and leucine-rich repeats in a mosaic G-protein-coupled receptor (GPCR). |
| Databáze: | OpenAIRE |
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