Contents

Databases

• Generalized databases (DNA, proteins and carbohydrates, 3D-structures)
• Specialized databases (EST, STS, SNP, RNA, genomes, protein classes, pathways, microarray data ...)

Database search

• Text-based database search (SRS, Entrez ...)
• Sequence-based database search (sequence similarity search) (BLAST, FASTA...)
• Motif-based database search (ScanProsite, eMOTIF)
• Structure-based database search (structure similarity search) (VAST, DALI...)

Analysis tools

• DNA sequence analysis tools
• RNA analysis tools
• Protein sequence and structure analysis tools (primary, secondary, tertiary structure)
• Tools for protein function assignment
• Phylogeny
• Microarray analysis tools

Miscellaneous

• Literature search
• Patent search
• Bioinformatics centers and servers
• Links to other collections of bioinformatics resources
• Medical resources
• Bioethics
• Protocols
• Software
• (Bio)chemie
• Educational resources

   

Primary sequence databases

 

EMBL (European Molecular Biology Laboratory nucleotide sequence database at EBI, Hinxton, UK)
GenBank (at National Center for Biotechnology information, NCBI, Bethesda, MD, USA)
DDBJ (DNA Data Bank Japan at CIB , Mishima, Japan)

 

Protein sequence databases

 

SWISS-PROT/TrEMBL (Swiss Institute of Bioinformatics, SIB, Geneva, CH)
PIR (Protein Information Resource, NBRF, Georgetown, USA)
PRF (Protein Research Foundation, Osaka, Jp)

 

Carbohydrate databases

 

CarbBank (Complex carbohydrate structure database, CCSD, at University of Georgia, USA, discontinued!)

 

3D structure databases

 

PDB (Protein Data Bank cured by Research Collaboratory of Structural Bioinformatics By Rutgers, SDSC and NIST, USA)
EBI-MSD (Macromolecular Structure Database at EBI, UK)

NDB (Nucleic Acid structure Datatabase at Rutgers University , USA)

Specialized sequence databases

 

dbEST (Database of Expressed Sequence Tags at NCBI, USA)

ESTs@EBI (Database of aligned and clustered ESTs at EBI,UK)

Bodymap (Human and mouse genome expression database (ESTs) at University of Tokyo, JP)

dbGSS (Database of Genome Survey Sequences at NCBI, USA)
dbSNP (Database of Single Nucleotide Polymorphisms at NCBI, USA)
dbSTS (Database of Sequence Tagged Sites at NCBI, USA)
HGBASE (Human genome sequence variations database, Karolinska Institute, EBI and EMBL consortium)

• RNA databases
ssu rRNA database (at UIA, Antwerp, Belgium)
lsu rRNA database (at UIA, Antwerp, Belgium)
RDP (Ribosomal database Project, Michigan State University, USA)
Other RNA databases

 

Genome databases

 

• Collections

GOLD (Genomes On Line Database: list of all complete and ongoing genome projects worldwide at University of Illinois, USA)
Organism Specific Databases (at CMS Molecular Biology Resource, SDSC, USA)
Entrez/Genome (NCBI, USA)

TIGR Database (TDB) (The Institute for Genomic Research, Rockeville MD, USA)
Microbial Genomes (Completed microbial genomes in GenBank and links to genomes in progress)
TIGR Microbial Database
PEDANT (Browse computationally analyzed completed and unfinished genomes at MIPS, Munich, Germany)
HAMAP (Highly automated microbial annotation of proteins at ExPaSy, CH)
UK CropNet (UK Crop Plant Bioinformatics Network, at JIC, IGER, NASC and SCRI, UK)
Demeeter's Genomes (Plant genome database at USDA-ARS Center for Bioinformatics and Comparative Genomics, Cornell University)
ArkDb (Livestock animal genome and mapping database at Roslin Institute, Edinburg, UK)

GeneCensus (Comparative genomics database at Yale University, USA)

• Model organism databases
Escherichia coli

E. coli Genome Center (Wisconsin University, USA)

The E. coli index (University of Birmingham, UK)

S. cerevisiae (Baker's yeast)

SGD (Yeast genome database at Stanford, USA)

MYGD (MIPS yeast genome database, Munchen, Germ.)

YPD (Yeast Protein Database at Proteome Inc., Boston, USA)

Arabidopsis thaliana

MATDB (MIPS A. thaliana database, Munich, Germ.)

TAIR (The Arabidopsis Information Resource, previously AtDB, at Stanford, USA)

KAOS (Kazusa Arabidopsis data Opening Site at Kazusa DNA Research Institute, Jp)

Arabidopsis Genome Analysis (at Cold Spring Harbor laboratories, USA)

TIGR Arabidopsis thaliana Database (TIGR, Rockeville MD, USA)

Oryza sativa (Rice)

INE (Integrated rice genome explorer: common database of the International Rice Genome Sequencing Project, IRGSP, Jp)

Caenorhabditis elegans

WormBase (C. elegans database at Cold Spring Harbor Laboratories, USA)

ACEDB (C. elegans genome database at the Sanger Centre, UK)

WormPD (C. elegans proteome database at Proteome Inc., Boston, USA)

Drosophila melanogaster (Fruit fly)

FlyBase (Drosophila genome database)

BDGP (Berkeley Drosphila genome project)

Mus musculus (Mouse)

MGI (Mouse genome informatics)

Homo sapiens

GDB (The human Genome Database, Toronto, Canada)

Ensembl (Automatically annotated human genome at EBI, UK)

Entrez-genome (Human genome at NCBI, USA)

Human genome working draft (Assembly of the current genome draft at the University of California Santa Cruz, USA)

HGP (Human Genome Project at the Sanger Centre, Cambridge, UK)

 

 

Specialized protein databases

 

TRANSFAC (Transcription Factor Database)
GCRDb (G-Protein Coupled Receptor Database)
PKR (Protein Kinase Resource)
MITOP (MITOchondria Project, database mitochondria-related genes, proteins and diseases at MIPS, Munich, Germany)
ENZYME (Enzyme database at ExPASy, CH)
MEROPS (Protease database at Babraham Institute, UK)
Prolysis (Protease and inhibitors database, Univ of Tours, Fr)
PROMISE (Prostetic groups and Metal Ions in protein active sites database at Leeds Univ., UK)
ReLiBase (database system for analysing receptor/ligand complexes deposited in the Protein Data Bank at EBI, UK)
IMGT (ImMunoGeneTics database of Igs, TcRs, and MHC molecules at Montpellier, France)
ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)
REBASE (Restriction enzyme database at New England Biolabs, USA)

• Protein classification databases
ProtoMap (Hierarchical classification of all Swiss-Prot proteins)
Proweb (Guide to specific protein families)
Pfam (Protein families database of alignments and HMMs at the Sanger Centre, UK)
PROTFAM (Protein classification at MIPS, Germany)
SCOP (Structural Classification of Proteins according to familiy, superfamily, common fold, and class)
CATH (Protein structure classification based on Class, Architecture, Topology, and Homologous superfamilies)
BioSpace (Unified sequence-structure classification of proteins, Stanford, USA)
LPFC (Library of Protein Family Cores)
FSSP (Fold classification based on structure-structure alignment of proteins, at EBI, UK)
ENZYME (Enzyme nomenclature database at ExPASy, CH)
Enzyme Structures Database (University College London, UK)
PRESAGE (Annotated protein structure database at Stanford University, USA)
CDD (Conserved Domain Database at NCBI, USA)

Specialized structure databases

Protein-Nucleic Acid Recognition Database (at Riken Gene Bank, Tsukuba, Jp)

3DInSight (Integrated database for structure, property and function of biomolecules at Riken Gene Bank, Tsukuba, Jp)

MolMovDB (Database of macromolecular movements at Yale University, USA)

Pathway databases

KEGG (Kyoto Encyclopedia of Genes and Genomes at Kyoto Univ. Jp. or at mirror servers)
LIGAND (Chemical database for emzyme reactions at Institute for Chemical Research, Kyoto Univ. Jp)
BRITE (Biomolecular Relations in Information, Transmission and Expression, Kyoto Univ., Jp)
Boehringer Mannheim - Biochemical pathways (Maintained at ExPASy, Ch)
EcoCyc & MetaCyc (Species-specific integrated pathway/genome databases, Pangea Systems. Registration required)
WIT  (What is There? Integrated pathway/genome database. Registration required)
UM-BBD (Microbial biocatalysis/biodegradation pathways, University of Minnesota, USA)
BRENDA (Enzyme and metabolic database at Univ Cologne, Germany)
SRS (Metabolic pathway database search at EBI, UK)

 

Microarray databases

ArrayExpress (Public repository for microarray based gene expression data at EBI, UK)
GEO (Public repository for microarray based gene expression data at NCBI, USA)

Lists of databases

 

DBCAT (Catalog of more than 500 molecular biology databases at INFOBIOGEN, France )
NAR 28 (1) 2000 (Nucl. Acids Res. biological database issue, papers available through NAR online)

SRS6 (Search EMBL, SWISS-PROT, TrEMBL, PIR, PDB, etc. at EBI, UK or other SRS5 Servers world wide)
ENTREZ (Integrated database search for nucleotides, proteins, genomes, structures, populations sets and literature at NCBI, USA)
DBGET/LinkDB(Integrated database search of LinkDB at GenomeNet, Kyoto University and University of Tokyo)

SSS (Sequence and structure searching site at Berkeley, US)
Molecules R US (Full text search of the PDB database at NIH)

MIA(Molecular Information Agent searching biological databases to find the existing information about a macromolecule at SDSC, USA)

FASTA (Fasta or fastx search at EBI, UK)
BLAST (Basic local alignment search tool at NCBI, USA)
BLAST (Blast at EMBn@t.CH)
BLAST Microbial Genomes (Search finished and unfinished genomic sequences at NCBI)
PSI BLAST (Position Specific Iterated Blast search at NCBI)
Genome and proteome FASTA (at EBI, UK)
Protein search in genomes (Blast and Fasta Species-specific protein sequence searches at Baylor College of Medecine, USA)
SectionSearch (FastA or TFastA search against predefined sections of sequence databanks at IUBIO Indiana, USA)
NRL-3D (Sequence-structure data base search at John Hopkins University, USA)

ScanProsite (Find Protein sequences matching PROSITE or other patterns at ExPASy, CH)
eMOTIF Scan (Find protein sequences matching EMOTIF patterns at Stanford University, USA)

3dSEARCH (Search structural homology of a query protein (PDB code) and visualize superposed 3D structures at Stanford University, USA)
Search_SCOP (Protein structure similarity search in SCOP database)
VAST (Structure-structure similarity search at NCBI, US)
DALI (Protein structure comparison with PDB at EBI,UK)
Finding 3D Similarity by CE (Combinatorial Extension) or CT (Compound Likeness) method at SDSC, USA)
LIBRA (Search sequences homologous to a given structure by Inverse Folding Protocol at NIG, Jp)

Restriction; Detect repeats and unusual patterns

Webcutter (Restriction analysis)
RepeatMasker (Search interspersed repeats and low complexity sequences)
Dot Plot (Compare a large sequence with itself at Virtual Genome Center)
Blast 2 Sequences (Compare two sequences <150 kb to trace repeat sequences)
LALIGN (Finds multiple matching subsegments in two sequences at EMBnet, Swiss node)
Zinfo (Detection of unusual sequences in large DNAs at Virtual Genome Center), USA)

Align sequences

Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
MAP (Multiple alignment of (long) sequences without penalizing large gaps)
ClustalW (Multiple sequence alignement at WUSTL, USA)
ClustalW (at EBI, UK)
ClustalW (at the Baylor College of Medicine, USA)
Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
AMAS (Analyze multiple aligned sequences at Oxford University, UK)
CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)

Find genes

Webtrans (Translation and codon usage of very large sequences at Virtual Genome Center)
Sixframe (Translate DNA sequence in all 6 possible frames)
ORF Finder (at NCBI)
GeneMark (Species-specific search for genes with WebGeneMark, WebGeneMark.hmm and Heuristic GeneMark at Georgia Institute of Technology , USA)
GeneMark (Species-specific search for genes cfr. WebGeneMark at EBI, UK)
GRAIL (Exon recognition USA).
Gene feature (Exon recognition, Promoter and Transcription Factor Binding Site Prediction, Open Reading Frame Identification.at Baylor College of Medicine (USA):
GenLang (Exon recognition at University of Pennsylvania, USA).
NetPlantGene (Prediction of splice sites in Arabidopsis at CBS, Denmark)
AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)

Find transcriptional elements

Identification of Prokaryotic Promoters (Promotor prediction in <100 kb DNA at Lawrence Berkeley National Laboratory, USA)
SignalScan (Identification of transcriptional elements in <100 kb DNA sequences < 100 kb at BIMAS, University of Minesota, USA)
IHF Site/Sigma 54 Promoter searches (at Pensylvania State University, USA)

Find tRNA

tRNAscan-SE (Search for tRNA genes in genomic sequence at Washington University, St Louis, US)
FAStRNA (Predict potential tRNA genes in genomic sequences at Institut Pasteur, Paris, Fr)

Other tools

MAR-Finder (Search for matrix association regions at NCGR, Santa Fe, USA)

Reverse Complement (Convert DNA sequence data to it's Reverse Complement.)

DNA folding server (Fold secondary structures)
PRIDE (Primer design atDFKZ, Heidelberg, Germany)
Netprimer (Free online primer analysis at Premier Biosoft Int., Ca, USA)
PCR primer selection
Primer3 (PCR primer selection tool at Whitehead Institute for Biomedical Research, US)

RNA Fold (Fold your own RNA sequences)
RNA World (Links to RNA resources from IMB Jena Biocomputing Group, Jena, Germ.)

Physicochemical properties

 

ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)

 

Analyse primary sequence

 

ProtColourer (Make colour-coded representation of an amino acid sequence at EBI)
Hydropathy plots (At Pensylvania State University, Department of Biochemistry and Molecular Biology)
ProtScale (Hydrophobicity, other conformational parameters, etc. at ExPASy)
SAPS (Statistical Analysis for charge clusters, repeats, hydrophobic regions, compositional domains etc. at ISREC, CH)

SignalP (Prediction of peptide signal sequence at CBS, Denmark)
TargetP (Prediction of subcellular localization at CBS, Denmark)
PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
NetOGlyc (Prediction of O-glycosylation sites in mammalian proteins at CBS, Denmark)
DGPI (Prediction of GPI-anchor and cleavage sites)
NetPhos (Prediction of phosphorylation sites in eukaryotic proteins)
Helical Wheel (Representation of alpha-helical peptides)
Other primary sequence analysis tools at ExPaSy

 

Alignment

 

Blast 2 Sequences (Alignment of two protein sequences using BLAST at NCBI, USA)
SIM (Alignment of 2 protein sequences at ExPASy, Switzerland)
ClustalW (Multiple sequence alignement at WUSTL, USA)
ClustalW (at EBI, UK)
ClustalW (at the Baylor College of Medicine, USA)
Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
MAP (Multiple alignment of (long) sequences without penalizing large gaps
Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
AMAS (Analyze multiple aligned sequences at Oxford University, UK)

CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)
BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)

 

Predict secondary structure

 

TMpred (Prediction of membrane-spanning regions and their orientation at ISREC).
TMHMM (Prediction of transmembrane helices in proteins at CBS, Denmark)
SOSUI (Prediction of Transmembrane Regions, JP)
PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
DAS (Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method, Stockholm University)
HMMTOP (Prediction of transmembrane helices and topology of proteins at Hungarian Academy of Sciences)

PredictProtein (Protein secondary structure prediction at EMBL)
JPred (Protein secondary structure prediction at EBI)
Predator (Secondary structure prediction from single or multiple sequences at EMBL, Heidelberg)
HNN (Hierarchical Neural Network secondary structure prediction at NPS@, Lyon, France)
PSIpred (Protein secondary structure prediction at Brunel University, UK)
nnPredict (Protein secondary structure prediction at UCSF, CA, USA)
Other secondary structure prediction tools at ExPASy

BTPRED (Prediction of beta-turns at UCL, UK)
Coils (Prediction of coiled Coil regions Lupas' method at EMBnet-CH)
PairCoil (Prediction of coiled Coil regions, Bergers method)
MultiCoil (Prediction of coiled coil regions as dimeric or trimeric assemblies at WI, USA)

TOPS (Protein topology cartoon generation at EBI, UK)

 

Analyse and model 3D structure

 

• 3D viewers

RasMol (Free offline 3D viewer. Download)
Swiss-Pdb Viewer (Deep View) (Free offline 3D viewing and analysis application, tightly linked to Swiss-Model. Tutorial)
Chime (Browser plugin for structure view from MDL Chemscape)
Cn3D (Browser plugin for structure view used in ENTREZ/STRUCTURE from NCBI)
WebMol (Online 3D viewer at University of California, USA)
WebMol (Online 3D viewer at EMBL)

• 3D analysis
TOPS (Protein topology cartoon generation at EBI, UK)
DOMPLOT (Generate schematic diagrams of the structural domain organisation annotated by ligand contacts at University College London, UK)
3DB Browser (Structure database browser at Weizmann Institute of Science, Israel)
STRUCTURE (Molecular Modeling Database MMDB from ENTREZ at NCBI)
Predicting Protein 3D structure based on homologous sequence search (EMBL Heidelberg, Germany)
123 (Fold prediction by aligning (threading) to a (set of) structure(s)
LOCK (Compare 3D structures of query and target proteins (PDB codes) and visualize superposed 3D structures at Stanford University, USA)
DALI (Automated Protein Structure Alignment at EBI,UK)
LIBRA (LIght Balance for Remote Analogous proteins: search compatible structure of a target sequence by threading at NIG, Jp)
VAST (Structure-structure similarity search at NCBI, US)
ASC (Analytic Surface Calculation of PDB molecules at EMBL, Heidelberg)
MolSurfer (Calculate and navigate protein-protein interfaces at EMBL, Heidelberg)
Protein-Protein Interaction Server (UCL, UK)

• 3D homology modeling
CPHmodels (Structure prediction by comparative homology modeling at CBS, Denmark)
Swiss-Model (Automated protein modeling server at ExPASy, Switzerland)
3DCrunch (Browse database of modeled Swiss-Prot proteins at ExPASy, Switzerland)
FAMS (Fully Automated Modeling Service at Kitasato University, JP)
3D-Jigsaw (Comparative modeling server at Imperial Cancer Research Fund, London, UK )
SDSC1 (Protein structure homology modeling server at SDSC, US)
List of comparative modeling tools (at the Rockefeller University, NY, USA)

Search for patterns, motifs, profiles, domains, families

 

ScanProsite (Search a protein sequence against PROSITE pattern database at ExPASy, CH)
PROSCAN (Search a protein sequence against PROSITE pattern database allowing mismatches at PBIL, Lyon, Fr)
PPSearch (Search a protein sequence against PROSITE pattern database with graphical output at EBI, UK)
PFSCAN (Search protein against different profile databases at ISREC; also searches PROSITE and Pfam patterns)
FingerPRINTScan (Search a protein sequence against protein motif fingerprints database PRINTS)
BLOCKS Search (Search a protein against BLOCKS database; also searches PRINTS)
SearchPfam at Wustl or EBI (Search a protein against Pfam domain/family database)
InterPro Search (Search a protein against the integrated protein domains and functional sites database InterPro at EBI, UK)
CD-Search (Search a protein against CDD domain database, including Pfam and SMART, with RPS-BLAST at NCBI, USA)
COGnitor (Search a protein agains the COG database at NCBI)
eMOTIF Search (Assign putative function to new proteins by sequence comparison with IDENTIFY motif database at Stanford University, USA)
SMART (Simple Modular Architecture Research Tool at EMBL; also searches Pfam)
PROCAT (Search a protein structure agains the PROCAT database of 3D enzyme active site templates)

MEME (Multiple EM for Motive Elicitation: Motive discovery at San Diego Supercomputer Centre, SDSC, Ca, USA)
Meta-MEME (motive buiding at San Diego Supercomputer Centre, SDSC, Ca, USA)
eMOTIF Maker (Generate motifs that describe protein families or superfamilies ats Stanford University, USA)

ProDom (Protein domain database at Toulouse, Fr)
DOMO (homologous protein domain families database)
Modules (mobile protein domains database)
SBASE (Protein domain library at ICGEB, It)

HSSP (Database of homology-derived structures and sequences of proteins at EBI)
3Motif (Find protein (domain)s with defined 3D motifs at Stanford University, USA (runs only with Netscape and Chime plugin))
eMATRIX Search (Function prediction by sequence analysis using minimal-risk scoring matrices at Stanford University, USA)
GeneQuiz (Automated analysis of protein sequences at EMBL)

Search and computation of pathways

KEGG (Search and computation tools at KEGG pathway database, Kyoto, Jp)

Protein-protein interactions

DIP (Search Database of Interacting Proteins at UCLA, USA)

ProNet Online (Database of interacting proteins from Myriad Genetics, US)

BIND (Biomolecular Interaction Network Database at the Samuel Lunenfeld Research Institute, Toronto, Canada)

Protein Annotation

PAA (Protein Annotator's Assistant at EBI, UK)

AAT (Analysis and Annotation Tool for finding genes in genomic sequences at Michigan Tech, USA)

Automatic alert for related new sequence

Sequence Alerting System (E-mail alert for daily searched new homologues of query sequence at EMBL, Heidelberg)
PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases at Trinity College Dublin, Ireland)
Swiss-Shop (Automatically receive alerts upon new submissions of related protein sequences)
Microbial Genomes Notification (Receive notifications by e-mail about new complete genomes in GenBank)

Multiple sequence alignment

 

ClustalW (Multiple sequence alignement at WUSTL, USA)
ClustalW (at EBI, UK)
ClustalW (at the Baylor College of Medicine, USA).
Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
AMAS (Analyze multiple aligned sequences at Oxford University, UK).
BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)
Entrez-PopSet (Search set of DNA sequences from populations of related individuals/organisms at NCBI)
Phylogeny software

 

Organism classification

NCBI Taxonomy
The Tree of Life Project
TreeBASE

ClustArray (DNA microarray data analysis at CBS, Denmark)
Expression Profiler (Microarray data analysis at EBI, UK)
TBI Expression Analysis (Find differential genes between two filter hybridisation experiments at DFKZ, Heidelberg)

PubMed (Search public version of full Medline integrated in ENTREZ at NCBI, USA)
PubMed Central (New! Free online access to full text of life Science rechearch articles at NCBI, USA)
MEDLINE + (Search and order full text Medline documents at Healthgate, USA)
LibriVision (Search Current Contents, Medline and more at KULeuven library. Access restricted to KULeuven)
LIBIS (Search in Belgian Library catalogues. Registration required)
PubCrawler (Automated alerting service that scans daily updates to PubMed and GenBank databases at Trinity College Dublin, Ireland)

esp@cenet (Search for National and worldwide patents at European Patent Office)
USPTO (Search for US patents at US Patent and Trademark office)
DPD (DNA Patent Database at Georgetown University, US)

ANGIS (Australian National Genomic Information Service)
BEN (Belgian EMBNet Node)
Biology Workbench
Brutlag Bioinformatics Group (at Stanford University, USA)
CBCG (USDA-ARS Center for Bioinformatics and Comparative Genomics)
CBS (Center for Biological Sequence analysis, Denmark)
CIB (Center for Information Biology, Mishima, Jp)
EBI (European Bioinformatics Institute, Hinxton, UK)
EMBnet and related WWW servers
ExPASy (Geneva, CH)
Genestream II (at IGH, Montpellier, Fr)
GenomeNet Japan
IBC (Institute for Biomedical computing, Washington University Seattle, USA)
ISCB (International Society for Computational Biology)
ISREC (Swiss Institute for Experimental Cancer Research)
MBCR (Molecular Biology Computation Resource)
MIPS (Munich Information Centre for Protein Sequences, Munich, Germ.)
NCBI (National Center for Biotechnology Information, Bethesda MD, USA)
NCGR (National Center for Genome Resources, Santa Fe, New Mexico, USA)
Roslin Institute Bioinformatics (Edinburg, UK)
Sanger Centre (Hinxton, UK)
SDSC (San Diego Supercomputer Center, USA)
SIB (Swiss Institute for Bioinformatics, Geneva, CH)
SSS (Sequence and Structure Searching site at Stanford, USA)
Stanford DNA Sequencing & Technology Center
Stanford Genomic Resources
TIGR (The Institute for Genomic Research, USA)
UCL Biochemistry BSM Group (UK)
VCG (Virtual Genome Center)

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Links to other collections of bioinformatics resources

[Back to Contents]

BCM Search Launcher (Interface for related WWW tools at Baylor College of Medicine)
GenomeWeb (at UK HMGP Resource centre, Hinxton, UK)
Pise-EMBOSS (GUI to EMBOSS, the European Molecular Biology Open Softaware Suite)
DNA and Protein Analysis Tools Collection (at Tigem, Italy)
AMOS' WWW Page Links (more than 1000 links by Amos Bairoch)
ExPASy Tools (CH)
CMS Molecular Biology Resource (at San Diego Supercomupter Center, US)
Bioinformatica (the ultimate (?) hub for bioinformatics)
Pack of WWW Tools for Molecular Analysis
Molecular Monte Carlo home page (at The Cooper Union, NY, USA)
ABIM online Analysis Tools (Marseille, Fr)

Other Molecular Biology Resources

OMIA (Online Mendelian Inheritance in Animals)
OMIM  (Online Mendelian Inheritance in Man)
THE MERCK MANUAL  (Guide to clinical information)

BIO (Biotechnology Industry Organization)

Protocol Online (Find/submit protocols in molecular biology, cell biology, immunology etc.)
Molecular Biology Protocols (collections of protocols)

BioCatalog (Software directory of general interest in molecular biology and genetics at EBI, UK)
Molscript
Molecular Simulations Inc. (MSI WebLab)
Logicieles (Software directory at Institut Pasteur with links to providers and tutorials)
Bio-Soft Ring
NCBI Toolbox (NCBI software tools for building bioinformatics resources)
Phylogeny Programs (Collection of phylogeny software and servers)
BioPerl (international association of developers of open source Perl tools for bioinformatics, genomics and life science research)

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(Bio)chemistry

[Back to Contents]

NIST Standard Reference Data Products Catalog
Searching for Something?
Webmolecules (Collection of 3D models for over 200.000 biomolecules)
Chemscape Main Page
ChemFinder Searching
QSAR (biological and physical-organic chemistry database at Medchem, Pomona College, USA)

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Educational resources

[Back to Contents]

BioComputing Hypertext Coursebook (Bielefeld, Germany)
Guide to Molecular Sequence Analysis (By Andrew Louka, Brunel University, Londen, UK)

Molecules in the Classroom/UMass Amherst
DNA Structure - Contents
NDB Biomolecular Resource (Nucleic Acid Database. 3D structures)
NDB Atlas of Nucleic Acid Containing Structures
Teachers' Molecular Visualization Resources
BioMolecular Structure Education Web Sites
Biochemical Tutorials in Chime
Biochemistry in 3d (Accompanies Lehninger Principles of Biochemistry)
IMAGE (Image library of biological macromolecules from IMB Jena Biocomputing Group, Jena, Germ.)
Protein Crystallography on the Web (University of London, UK)

Under Constructon ...