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FIMM


NAR Molecular Biology Database Collection entry number 150

Database Description

FIMM is an integrated database of functional molecular immunology that focuses on the T-cell response to disese-specific antigens. FIMM provides fully referenced information integrated with data retrieval and sequence analysis tools on HLA, peptides, T-cell epitopes, antigens, diseases and constitutes one backbone of future computational immunology research. More than 480 new entries were added and 150 updated since the first release. Protein antigens are sources of T-cell epitopes or naturally processed peptides and contain sequences and feature information linked to SWISS-PROT and GenBank. Antigen protein data have been enriched with more than 27,000 sequences derived from the non-redundant SwissProt-TREMBL-TREMBL_NEW (SPTR) database of antigens similar or related FIMM antigens across various species to facilitate a comprehensive analysis of conserved or variable T-cell epitopes. Protein antigens are linked to peptide and disease entries. Peptide entries, which contain information naturally processing, binding to HLA molecules and cytotoxicity are linked to protein antigen and HLA entries. Source antigens could not be identified in 11% (N=164) of the peptides. Most of the unknown peptides may represent products of yet uncharacterized functional genes. HLA entries include information about sequence, binding pockets, TcR and CD8 binding sites. HLA entries are linked to relevant peptide and disease entries including data about disease etiology, HLA-disease associations, and links to HLA and protein antigen entries. Integrated text and sequence-based analysis tools include keyword search, pattern search using regular expressions, Blast2, ClustalW multiple sequence alignment, and HLA pocket and TCR contact site analysis. Text-based search results are reported in tabular format containing hyperlinks to other entries of FIMM and when applicable to external databases GeneCards, OMIM, Genatlas, IMGT and PubMed among other specialized disease information sources.


Go to the abstract in the NAR 2002 Database Issue.
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