Working page |
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The sixteen institutions that form the
Human Genome Sequencing Consortium include:
Baylor College | Baylor College of Medicine, Houston, Texas, USA |
Beijing HGC | Beijing Human Genome Center, Institute of Genetics, Chinese Academy of Sciences, Beijing, China |
Braunschweig GBF | Gesellschaft für Biotechnologische Forschung mbH, Braunschweig, Germany |
Genoscope | Genoscope, Evry, France |
Waltham GTC | Genome Therapeutics Corporation, Waltham, MA, USA |
Jena IMB | Institute for Molecular Biotechnology, Jena, Germany |
Joint Genome | Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA, USA |
Keio University | Keio University, Tokyo, Japan |
Max Planck | Max Planck Institute for Molecular Genetics, Berlin, Germany |
RIKEN | RIKEN Genomic Sciences Center, Saitama, Japan |
The Sanger Centre | The Sanger Centre, Hinxton, U.K. |
Stanford TDC | Stanford DNA Sequencing and Technology Development Center, Palo Alto, CA, USA |
Washington Univ. Genome Center | University of Washington Genome Center, Seattle, WA, USA |
Washington Univ. Mult. Seq. Center | University of Washington Multimegabase Sequencing Center, Seattle, WA,USA |
Whitehead Institute | Whitehead Institute for Biomedical Research, MIT, Cambridge, MA, USA |
Washington Univ. Genome Seq. Center | Washington University Genome Sequencing Center, St. Louis, MO, USA |
Computational support and analysis (Consortium):
NCBI | The National Center for Biotechnology Information at NIH |
EBI | The European Bioinformatics Institute in Cambridge, UK |
Celera:
Celera Genomics | Celera Genomics (A PE Corporation Business) homepage. |
Non-Human Genome Projects
Mouse | Mouse Genome Informatics |
Microbial | The TIGR Microbial Database |
Parasite | Parasite Genome |
Arabidopsis | The Arabidopsis cDNA Sequence Analysis Project |
Mosquitoes | The Mosquito Genomics WWW Server |
C. elegans | Wormbase |
Drosophila | Flybase |
Rat | RATMAP |
Saccharomyces | Saccharomyces Genome Database |
GeneQuiz | GeneQuiz is an integrated system for large-scale biological sequence analysis. (EBI) |
DANTE | DANTE: Viral genomes analysis. (PDG-CNB) |
COGs | Clusters of Orthologous Groups of proteins: Phylogenetic classification of proteins encoded in complete genomes |
GenProtEC | GenProtEC: database dedicated to E. coli genome and proteome |
MicrobioNet | MICROBIONET: Provide information on some of the thousands of forms of bacteria. |
TIGR | TIGR Microbial Database: microbial genomes completed and in progress |
GOLD | GOLD: Genomes OnLine Database HomePage |
GenomeNet | GenomeNet WWW server (KEGG, DBGET, ...) |
Beowulf | Wellcome Trust Beowulf Genomics Initiative |
Human genome guides:
NCBI-HumanGenome | Human genomic sequence and gene annotation at NCBI. |
GoldenPath | Human Genome Project Working Draft at University of California at Santa Cruz. |
Ensembl | Ensembl, a joint human genome annotation project of the EBI and the Sanger Centre. |
MBS | MBS - Molecular Biology On-line tools selection |
Bio-Web | The Bio-Web: DNA and Protein Sequence Analysis Tools |
FBS | FRONTIERS IN BIOSCIENCE; DNA/RNA ANALYSIS TOOLS |
Deambulum | The DEAMBULUM (Computing applied to biomolecules and genomes) : nucleic acid sequence analysis |
Adelaide | A Pack of Molecular Analysis Tools. Adelaide University |
ExPASy | ExPASy Proteomics Tools: A collection of tools for DNA and Protein analysis and manipulation (ExPASy, Switzerland) |
PIR | Protein Information Resource Home Page (Georgetown University) |
BIOWEB | Biological software at the Institut Pasteur (Blast, ClustalW, Phylip, HMM, and much more) (France) |
SRS5 - EMBL | SRSWWW server at EMBL, Heidelberg, Germany. , version 5.1.0 |
SRS6 - CNB | SRSWWW server at EMBnet/CNB , version 6.0.7.2 |
SRS6-EBI | SRSWWW server at EBI, Hinxton, UK., version 6.0.6 |
MORE PUBLIC SRS SERVERS | Links to public SRS servers, libraries and applications. |
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 BLAST2 (blastall) search at NCBI |
Blast2_ISREC | Advanced BLAST2 search at ISREC, CH |
Blast Unfinished | Blast to Unfinished microbial genomes at NCBI |
Blast2_nrdb90 | Similarity search by against nrdb90 (at EBI) |
ProtEST | Search the Expressed Sequence Tag database (EBI) |
Psi-Blast_NCBI | Psi-Blast at NCBI |
FASTA3_EBI | FASTA3 at EBI |
FDF | Fast Data Finder (Smith-Waterman) at ISREC |
WWW-Query | WWW-Query: Keyword + ClustalW search and alignment (PBIL in Lyon, France) |
Search and Cluster | Recursive BLAST-searches and NCUT-clustering (PDG-CNB) |
BLAST 2 sequences | BLAST 2 sequences against each other (at NCBI) |
SIM | Alignments between two protein sequences or within a sequence (ExPASy, CH) |
ClustalW_EMBL | CLUSTAL W (1.75) Multiple Sequence Alignments (EMBL-ES) |
ClustalW_EBI | ClustalW Server at EBI |
ClustalW_BioWeb | ClustalW Server at the Institut Pasteur (France) |
T-COFFEE | T-Coffee: Accurate, but slow, Multiple Sequence Alignment server (EMBNET.CH) (limit: 30 seq, 1000 res) |
T-COFFEE | T-Coffee: Cedric Notredame page (University of Nijmegen, NL) (limit: 20 seq 300 res) |
CMBI_Tree_Plot | CMBI Phylogenetic Tree Plot Server (University of Nijmegen, NL) (GIF, PS,.. trees) |
Phylodendron | Phylodendron: Phylogenetic tree printer (EMBL-ES) |
PHYLIP | PHYLIP is a free package of programs for inferring phylogenies (Whasington Univ.) |
WebPHYLIP | WebPHYLIP is a web version of the original PHYLIP package. National University of Singapore. |
BioWebPHILIP | PHILIP (web version) at the Institut Pasteur (France) |
PAUP | PAUP is a software package for inference of evolutionary trees (Florida Stat. Univ.) |
Philogeny Programs | Here are some 193 of the phylogeny packages, and 16 free servers. |
Phylogeny Course | Molecular Systematics and Evolution Course (London - Rio de Janeiro) |
Gene Prediction | A collection of tools suitable for gene prediction (EMBL) |
EBI Services | Database Searching, Browsing and Analysis Tools (EBI) |
ExPASy Tools | ExPASy Proteomics tools |
AQUA | AQUA - Alignment Quality Assessment (EMBL) |
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 |
HMMER (restricted) | HMMER 2.1.1 Profile hidden Markov models for biological sequence analysis |
HMMER at BioWeb | HMMER : using HMM (Hidden Markov Model) (Sean Eddy) at the Institut Pasteur (France) |
NAIL | Network Analysis Interface for Linking HMMER results (EMBL) |
Primary structure.
Prosite | ProfileScan Server (ISREC, CH) |
ProDom | ProDom protein domain database (INRA, FR) |
InterPro | Integrated resource of protein domains and functional sites. (EBI, UK) |
PFAM | Protein families database of alignments and HMMs (Sanger, UK) |
DART | Domain Architecture Retrieval Tool (It shows similar domain achitectures, too) (NCBI) |
PRINTS | Protein Motif Fingerprint Database (UCL, UK) |
SMART | Simple Modular Architecture Research Tool. Domains/motif detection (EMBL) |
Blocks/Prints | Searching both Blocks+ and Prints databases (FHCRC, USA) |
SignalP | Predicts the presence and location of signal peptide (CBS, DK) |
PredictProtein | The PredictProtein server (Columbia, USA) |
PredictProtein (local) | The PredictProtein server (EMBnet / CNB, ES) |
ExPASy Tools | ExPASy Proteomics tools |
Protein families / classification.
COG | Phylogenetic classification of proteins encoded in complete genomes (NCBI) |
ProtoMap | An automatic hierarchical classification of all swissprot proteins |
Search and Cluster | Recursive BLAST-searches and NCUT-clustering (PDG-CNB) |
Protein Kinases | Web accessible compendium of information on the protein kinase family of enzymes. |
PFAM | Protein families database of alignments and HMMs (Sanger, UK) |
InterPro | Integrated resource of protein domains and functional sites. (EBI, UK) |
ProDom | ProDom protein domain database (INRA, FR) |
Secondary structure.
EVAsec | EVA (evaluation of protein structure prediction servers in 'real time'): secondary structure |
TMHMM | Prediction of transmembrane helices in proteins (CBS, DK) |
HMMTOP | Prediction of transmembrane helices and topology of proteins (Inst. Enzymol. Budapest) |
SignalP | Predicts the presence and location of signal peptide (CBS, DK) |
COILS | Prediction of Coiled Coil Regions in Proteins (ISREC, CH) |
MultiCoil | Program for Predicting Two- and Three-Stranded Coiled Coils (MIT, USA) |
Jpred | A consensus method for protein secondary structure prediction (EBI, UK) |
Psi-Pred | Protein structure prediction server (secondary structure & transmembrane topology) (University College London, UK) |
APSSP | APSSP: Advanced Protein Secondary Structure Prediction Server (Chandigarh, INDIA) |
TOPS | Protein Topology Home Page (EBI, UK) |
SAM-T99 | SAM-T99 secondary structure prediction. |
PredictProtein | The PredictProtein server (Columbia, USA) |
PredictProtein (local) | The PredictProtein server (EMBnet / CNB, ES) |
ExPASy Tools | ExPASy Proteomics tools |
3D structure / Modeling / Threading
Homology modelling:
EVA-cm | EVA (evaluation of protein structure prediction servers in 'real time'): comparative modeling |
Swiss-Model | SWISS-MODEL. An Automated Comparative Protein Modelling Server (ExPASy, CH) |
SWISS-MODEL Repository | SWISS-MODEL Repository. A database for theoretical protein models (ExPASy, CH) |
WHATIF | WHAT IF Web interface: homology modelling, drug docking, electrostatics calculations, structure validation and visualisation. |
TITO/Modeller | Modeller at the CBS Bioinformatic Tools Server (Montpellier, France) |
CPHmodels | The CPHmodels Server using comparative (homology) modelling (BioCentrum, Denmark) |
SDSC1 | "SDSC1" - SDSC Protein Structure Homology Modeling Server (San Diego, USA) |
Threading:
EVAfr | EVA (evaluation of protein structure prediction servers in 'real time'): threading |
PredictProtein | The PredictProtein server (TOPITS) (Columbia, USA) |
PredictProtein (local) | The PredictProtein server (TOPITS) (EMBnet / CNB, ES) |
3D-PSSM | 3D-PSSM Protein Fold Recognition (Threading) Server (Imperial Cancer Res. Fund., UK) |
UCLA-DOE | UCLA-DOE Fold-Recognition server (UCLA, USA) |
Psi-Pred (GenThreader) | Protein structure prediction server (sequence profile based fold recognition) (University College London UK) |
SAM-T99 | SAM-T99 protein structure HMM library search. |
FFAS | Fold & Function Assignment System. (Burnham Institute, USA) |
Fold-Pred | Protein Fold Prediction in the context of SCOP. |
FUGUE | FUGUE Profile Library Search Against HOMSTRAD (Cambridge, UK) |
Threading Meta-Server | Threading Meta-Server at the CBS Bioinformatic Tools Server (Montpellier, France) |
Threading Meta-Server | Threading Meta-Server at BioInfo.PL (Warszawa, Poland) |
SAUSAGE | SAUSAGE: Protein threading with flexible force fields (Canberra, Australia) |
LOOPP | A program for potential optimization and alignments (Cornell, USA) |
Superfamily | HMM library and genome assignments server (Cambridge, UK) |
Structure validation:
AQUA | AQUA - Alignment Quality Assessment |
BIOTECH Validation Suite | Biotech Validation Suite for Protein Structures (PROCHECK, PROVE & WHAT IF) |
WHATIF | WHAT IF Web interface: homology modelling, drug docking,
electrostatics calculations, structure validation
and visualisation. |
3D Evaluation | Verify3D & PROSA II at the CBS Bioinformatic Tools Server (Montpellier, France) |
Databases:
PDB - EBI | Protein Data Bank (EBI) |
PDB - RCSB | Protein Data Bank (RCSB) |
PDBsum | Summaries and structural analyses of PDB data files (UCL, UK) |
Get ExPDB | Get ExPDB entries for a PDB code (Swiss-Model, ExPASy, CH) |
OCA | PDB advanced browser(EBI) |
PDBselect | Subset of the structures in the PDB that does not contain (highly) homolog sequences |
EC->PDB | Enzyme Structures deposited in PDB (UCL, UK) |
Prosite->PDB | PROSITE patterns in PDB entries (UCL, UK) |
Ligands->PDB | List of ligands bound to PDB srtuctures (UCL, UK) |
RELIBASE | Relibase: A program for searching protein-ligand databases. |
Molecular Models | 1400 Molecular Models (from chemistry) in .pdb format (Okanagan University College, Canada) |
NDB | The Nucleic Acid Database Project (UK) (Nucleic Acid Structures) |
IMB Jena | IMB Jena Image Library of Biological Macromolecules (Jena, Germany) |
CORINA | CORINA: A powerful and reliable tool for the generation of 3D atomic coordinates (Erlangen, Germany) |
Structural Genomics Targets | Targets For NIH Structural Genomics Projects (SEARCH for sequences) |
SCOP | Structural Classification of Proteins (MRC-LMB, UK) |
CATH | CATH Protein Structure Classification (UCL-BSM, UK) |
The Dali server | The Dali server: Network service for comparing protein (query) structures in 3D (EBI) |
WWWSUP | Pairwise Superposition of Protein 3D Structures (CIGB, Habana, Cuba) |
FSSP | Fold classification based on Structure-Structure alignment of Proteins (FSSP) (EBI) |
DaliDD | Dali Domain Dictionary: structural classification of protein domains (EBI) |
Homstrad | Homologous Structure Alignment Database (CrystBioc, UK) |
3Dee | 3 Dee - A Database of Protein Domain Definitions (EBI) |
CAMPASS | CAMbridge database of Protein Alignments organised as Structural Superfamilies (CrystBioc, UK) |
ProSup | Structure Comparison Server (Manfred J. Sippl - CAME) |
Contacts & Quaternary structure
EVAcon | EVA (evaluation of protein structure prediction servers in 'real time'): inter-residue contacts |
CORNET | Prediction of Residue Contacts in Proteins (CIRB Biocomputing Group, Bologna Univ. Italy) |
PDGCON | The threading server page from the Protein Design Group at the CNB (Madrid, Spain) |
SPIN-PP | Surface Properties of INterfaces - Protein Protein Interfaces (Columbia Univ. USA) |
PQS | Protein Quaternary Structure Database Searches at the EBI |
NDB | The Nucleic Acid Database Project (UK) (Protein/Nucleic Acid Complexes) |
Direct links to databases
EBI SRS BookmartLet (info) for: |
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