Main Bioinformatics Research Centers (USA & EUROPE):
| NCBI | The National Center for Biotechnology Information at NIH, USA |
| EBI | The European Bioinformatics Institute in Cambridge, UK |
Human Genome Project
| Joint Genome | Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA, USA |
| The Sanger Centre | The Sanger Centre, Hinxton, U.K. |
| BROAD Institute | BROAD Institute, MIT and Harvard, Cambridge, MA, USA |
| Washington Univ. Genome Seq. Center | Washington University Genome Sequencing Center, St. Louis, MO, USA |
Non-Human Genome Projects
| Mouse | MGI Mouse Genome Informatics |
| C. elegans | Wormbase |
| Drosophila | Flybase |
| Rat | Ratmap |
| Saccharomyces | SGD Saccharomyces Genome Database |
| SRS-EBI | SRS WWW server at EBI, Hinxton, UK., version 6.0.6 |
| Swiss-Prot | Access to SWISS-PROT and TrEMBL (ExPASy, CH) |
| ORF Finder | Open Reading Frame Finder (NCBI) |
| Blast2_EMBL | WU-BLAST2 search at EMBL (blast 2.0 with gaps) |
| Blast2_EBI | WU-BLAST2 search at EBI (blast 2.0 with gaps) |
| Blast2_NCBI | Basic/Advanced BLAST (blastall) search at NCBI |
| FASTA3_EBI | FASTA3 at EBI |
| ClustalW_EBI | ClustalW2 Server at EBI |
| SAM_Home | SAM: Sequence Alignment and Modeling System (HMM) |
| SAM_applications | UCSC HMM Applications |
| ISMB99 tutorial on using HMMs | Making the most of your hidden Markov models |
| NAIL | Network Analysis Interface for Linking HMMER results (EMBL) |
| AQUA | AQUA - Alignment Quality Assessment (EMBL) |
Primary structure
| InterPro | Integrated resource of protein domains and functional sites (EBI, UK) |
| SMART | Simple Modular Architecture Research Tool. Domains/motif detection (EMBL) |
| SignalP | Predicts the presence and location of signal peptide (CBS, DK) |
| PredictProtein | The PredictProtein server (Columbia, USA) |
| ExPASy Tools | ExPASy Proteomics tools |
Secondary structure
| COILS | Prediction of Coiled Coil Regions in Proteins (ISREC, CH) |
| PredictProtein | The PredictProtein server (Columbia, USA) |
| ExPASy Tools | ExPASy Proteomics tools |
Tertiary structure /
Threading
| Swiss-Model | SWISS-MODEL. An Automated Comparative Protein Modelling Server (ExPASy, CH) |
| UCLA-DOE | UCLA-DOE Fold-Recognition server (UCLA, USA) |
| PDB - RCSB | Protein Data Bank (RCSB) |
| PDBsum | Summaries and structural analyses of PDB data files (UCL, UK) |
| SCOP | Structural Classification of Proteins (MRC-LMB, UK) |
| CATH | CATH Protein Structure Classification (UCL-BSM, UK) |
| FSSP | Fold classification based on Structure-Structure alignment of Proteins (FSSP) (EBI) |
| KEGG | KEGG:Kyoto Encyclopedia of Genes and Genomes (ICR, JP) |
| REACTOME | Reactome is a database of biological pathways |
| PubMed | PubMed is the National Library of Medicine's search service |