Contents

Databases

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

Database search

• Text-based (SRS, Entrez ...)
• Sequence-based (sequence similarity search) (BLAST, FASTA...)
• Motif-based (ScanProsite, eMOTIF)
• Structure-based (structure similarity search) (VAST, DALI...)
• Mass-based protein search (ProteinProspector, PeptIdent, Prowl …)

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 (Swiss Institute of Bioinformatics, SIB, Geneva, CH)

TrEMBL (=Translated EMBL: computer annotated protein sequence database at EBI, UK)

PIR-PSD (PIR-International Protein Sequence Database, annotated protein database by PIR, MIPS and JIPID at NBRF, Georgetown University, USA)

UniProt (Joined data from Swiss-Prot, TrEMBL and PIR)

UniRef (UniProt NREF (Non-redundant REFerence) database at EBI, UK)

IPI (International Protein Index; human, rat and mouse proteome database at EBI, UK)

 

Carbohydrate databases

 

CarbBank (Former complex carbohydrate structure database, CCSD, discontinued!)

 

3D structure databases

 

PDB (Protein Data Bank cured by RCSB, USA)
EBI-MSD (Macromolecular Structure Database at EBI, UK )

NDB (Nucleic Acid structure Datatabase at Rutgers State University of New Jersey , USA)

Specialized sequence databases

 

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

TGI (TIGR Genome Indices, integrated analysis of public EST data, TIGR, USA)

Mendel ESTs (Database of annotated plant ESTs in dbEST at JIC, Norwich, 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)
SNPper (SNP explorer by Children's Hospital Informatics Program, Boston, USA)
dbSTS (Database of Sequence Tagged Sites at NCBI, USA)
HGVBASE (Human Genome Variation database, European consortium involving the Karolinska Institute (Sweden), EBI (UK) and EMBL (Germany)

 

• RNA databases

ssu and lsu rRNA database (European ribosomal database at University of Ghent, Belgium)

RDP (Ribosomal database Project, Michigan State University, USA)

miRNA Registry (microRNA registry at the Sanger Insitute, UK)

 

Genome databases

 

• Collections

GOLD (Genomes On Line Database: list of all complete and ongoing genome projects worldwide at University of Illinois, USA)

Genomes at NCBI (NCBI, USA)

Organism Specific Databases (at CMS Molecular Biology Resource, SDSC, 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)

PEDANT (Browse computationally analyzed completed and unfinished genomes at MIPS, Munich, Germany)

Ensembl (Automatically annotated genomes at EBI, UK)

GeneQuiz (Highly automated analysis of completed genomes at EBI, UK)

HAMAP (Highly automated microbial annotation of proteins at ExPaSy, CH)

UK CropNet (UK Crop Plant Bioinformatics Network, at JIC, IGER, NASC and SCRI, UK)

ArkDb (Livestock animal genome and mapping database at Roslin Institute, Edinburg, UK)

MITOP (MITOchondria Project, database mitochondria-related genes, proteins and diseases at MIPS, Munich, Germany)

Codon Usage Database (Organism specific codon usage database at Kazuasa DNA Research Institute, Jp)

 

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)

CYGD (MIPS Comprehensive Yeast Genome Database, Neuherberg, Germany)

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)

RGP (Rice Genome Research Programme, Jp)

Gramene (Comparative mapping resource for graines)

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)

Drosophila melanogaster (Fruit fly)

FlyBase (Drosophila genome database)

BDGP (Berkeley Drosphila genome project)

Danio rerio (Zebrafish)

ZFIN (Zebrafish Information Network at University of Oregon, USA)

WashU-Zebrafish Genome Resources (Zebrafish EST database at Washington University, USA)

Mus musculus (Mouse)

MGI (Mouse genome informatics)

Homo sapiens

GDB (The human Genome Database, Toronto, Canada)

HIB (HumanInfoBase of annotated UniGene clusters - putative human gene transcripts - at MIPS, Germany)

Human genome resources (at NCBI, USA)

Human genome browser (at the University of California Santa Cruz, USA)

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

GeneLinks (Portal to hyperlinks for each human gene at the Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden)

 

 

Specialized protein databases

 

• Proteome databases

Proteome analysis (comprehensive statistical and comparative analyses of the predicted proteomes of fully sequenced organisms at EBI, UK)

• Specific protein family databases

Proweb (Guide to specific protein families)

TRANSFAC (Transcription Factor Database, housed at Biobase)

GPCRDB (G-Protein Coupled Receptor Database)

PKR (Protein Kinase Resource)

ENZYME (Enzyme database at ExPASy, CH)

MEROPS (Peptidase database at Sanger Institute, UK)

Prolysis (Protease and inhibitors database, Univ of Tours, Fr)

CAZy (Carbohydrate-active enZymes at CNRS, Fr)

PROMISE (Prostetic groups and Metal Ions in protein active sites database at Scripps Researche Institute, USA)

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)

REBASE (Restriction enzyme database at New England Biolabs, USA)

 

• Protein classification databases

CluSTr (Clusters of SWISS-PROT and TrEMBL proteins at EBI, UK)

Pfam (Protein families database of alignments and HMMs at the Sanger Centre, UK)

TIGRFAMs (Protein families based on HMMs at TIGR, USA)

Hits (Protein domain database at ISREC, Switzerland)

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)

Dali (Dali Fold classification based on structure-structure alignment of proteins, at Helsinki University, Finland)

ENZYME (Enzyme nomenclature database at ExPASy, CH)

Enzyme Structures Database (University College London, UK)

PRESAGE (Annotated protein structure database at the University of California, Berkeley, USA)

CDD (Conserved Domain Database at NCBI, USA)

Specialized structure databases

Protein-Nucleic Acid Recognition Database (at BioInfo Bank, Jp)

3DInSight (Integrated database for structure, property and function of biomolecules at BioInfo Bank, 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)

BioCyc (Microbial species-specific integrated pathway/genome database)

WIT  (What is There? Integrated pathway/genome database. Registration required)

EMP (Database of Enzymes and Metabolic pathways public server

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 (Genome Expression Omnibus: Public repository for microarray based gene expression data at NCBI, USA)

2D-page databases

Gelbank (US department of Energy)

Swiss-2DPAGE (Swiss Institute of Bioinformatics, SIB, Geneva, CH)

Lists of databases

DBCAT (Catalog of more than 500 molecular biology databases at INFOBIOGEN, France )

NAR 31 (1) 2003 (Nucl. Acids Res. biological database issue, papers available through NAR online)

NAR 32 (1) 2004 (Nucl. Acids Res. biological database issue, papers available through NAR online)

ENTREZ (Integrated database search for nucleotides, proteins, genomes, structures, populations sets and literature at NCBI, USA)

SRS (Search EMBL, SWISS-PROT, TrEMBL, PIR, PDB, etc. at EBI, UK)

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)

BLAST (Basic local alignment search tool at NCBI, USA)

FASTA (Fasta or fastx search at EBI, UK)

MPsrch (Smith-Waterman algorithm-based search at EBI, UK)

BLAST Microbial Genomes (Search finished and unfinished genomic sequences at NCBI)

Genome and proteome FASTA (at EBI, UK)

PIR-NRL3D (Sequence-structure data base search at John Hopkins University, USA)

Kangaroo (Find sequences matching a given DNA or protein pattern at Mount Sinai Hospital, Toronto, Canada)

ScanProsite (Find protein sequences matching PROSITE or other patterns at ExPASy, CH)

ShapeSifter (Find protein sequences matching EMOTIF patterns 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)

ProteinProspector (Proteomics tools for mining sequence databases in conjunction with mass spectrometry at UCSF, USA)

PeptIdent (Protein identification using pI, Mw and peptide mass fingerprinting data at ExPaSy, CH)

Prowl (Resource for protein chemistry and mass spectrometry at the Rockefeller University NY, USA)

Mascot (Protein identification using mass spectrometry data by Matrix Science, London, UK)

MassSearch (Search SwissProt or EMBL by protein mass after digestion at ETH Zurich, CH)

Mowse (Search the owl protein sequence database with protein fragment information at the HGMP-RC, UK)

PeptideSearch (Protein identification by peptide mapping or peptide sequencing at the EMBL, Heidelberg, Germany)

Lutefisk (Software for the de novo interpretation of peptide CID spectra from Immunex, Seattle, USA)

Restriction; Detect repeats and unusual patterns

Restrictionmapper

Webcutter (Restriction analysis)

RepeatMasker (Search interspersed repeats and low complexity sequences)

REPuter (Fast computation of maximal repeats in complete genomes at Bielefeld University, Germany)

dnadot (Find regions of similarity in two sequences and repeats within a single sequence at Colorado State University, USA)

Blast 2 Sequences (Compare two sequences <150 kb to trace repeat sequences)

LALIGN (Finds multiple matching subsegments in two sequences at EMBnet, Swiss node)

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 (at EBI, UK)

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

Sixframe (Translate DNA sequence in all 6 possible frames at Baylor College of Medecine, USA)

ORF Finder (at NCBI)

GeneMark (Species-specific search for genes at Georgia Institute of Technology , USA)

GeneMark (Species-specific search for genes cfr. WebGeneMark at EBI, UK)

GenLang (Exon recognition at University of Pennsylvania, USA).

GeneMachine (Integrated comparative and predictive gene identification at NHGRI, 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/Eukaryotic 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)

FirstEF (first-exon and promoter prediction program for human DNA at CSHL, 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

CountCodon (Analyse codon usage in protein coding sequence at Kazuasa DNA Research Institute, Jp)

MAR-Wiz (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 at DFKZ, 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)

GeneFisher (Interactive PCR primer design tool at the University of Bielefeld, Germany)

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer design at the Weizmann Institute, Israel)

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)

ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)

 

Analyse primary sequence

 

ProtColourer (Make colour-coded representation of an amino acid sequence at EBI)

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, University of Geneva, CH)

NetPhos (Prediction of phosphorylation sites in eukaryotic proteins at CBS, Denmark )

Scansite (Prediction of phosphorylation sites and protein binding sites at MIT, Cambridge, USA)

Helical Wheel (Representation of alpha-helical peptides)

Other primary sequence analysis tools at ExPaSy

 

Alignment

 

• Pairwise

Blast 2 Sequences (Alignment of two protein sequences using BLAST at NCBI, USA)

SIM (Alignment of 2 protein sequences at ExPASy, Switzerland)

Pairwise sequence alignment (at Baylor College of Medecine, USA)

Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)

 

• Multiple

ClustalW (at EBI, UK)

ClustalW (at the Baylor College of Medicine, USA)

MAP (Multiple alignment of (long) sequences without penalizing large gaps)

Multiple sequence alignment (at Baylor College of Medecine, USA)

AMAS (Analyze multiple aligned sequences at Oxford University, UK)

• Editors

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)

TopPred2 (Topology prediction of membrane proteins at the Institut Pasteur, Paris, France)

 

PredictProtein (Protein secondary structure prediction at EMBL)

JPred (Protein secondary structure prediction at Dundee University, UK)

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 by Berger's method)

MultiCoil (Prediction of coiled coil regions as dimeric or trimeric assemblies at WI, USA)

TOPS (Protein topology cartoon generation at University of Leeds, 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)

 

• 3D analysis

TOPS (Protein topology cartoon generation at University of Leeds, UK)

DOMPLOT (Generate schematic diagrams of the structural domain organisation annotated by ligand contacts at University College London, UK)

OCA (Structure database browser at EBI, UK)

STRUCTURE (Molecular Modeling Database MMDB from ENTREZ at NCBI)

 

PsiPred (Sequence profile based fold recognition at Brunel University, UK)

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)

CE (3-D protein structure comparison and alignment using the combinatorial extension (CE) method at SDSC, 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 IMP, Vienna)

MolSurfer (Calculate and navigate protein-protein interfaces at EML, Germany)

Protein-Protein Interaction Server (UCL, UK)

 

• 3D homology modeling

CPHmodels (Structure prediction by comparative homology modeling at CBS, Denmark)

Swiss-Model (Automated protein homology-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, USA)

Meta PP (Collection of structure prediction services at Columbia University, USA)

List of comparative modeling tools (at the Rockefeller University, NY, USA)

Scan or search for patterns, motifs, profiles, domains, families

 

ScanProsite (Scan a protein sequence against PROSITE pattern database at ExPASy, CH)

PROSCAN (Scan a protein sequence against PROSITE pattern database allowing mismatches at PBIL, Lyon, Fr)

PPSearch (Scan a protein sequence against PROSITE pattern database with graphical output at EBI, UK)

PFSCAN (Scan protein against different profile databases at ISREC; also searches PROSITE and Pfam patterns)

FingerPRINTScan (Scan a protein sequence against protein motif fingerprints database PRINTS)

BLOCKS Search (Scan a protein against BLOCKS database; also searches PRINTS)

eMOTIF-Scan (Scan for motifs that describe protein families or superfamilies at Stanford University, USA)

Scansite (Prediction of protein signaling sequence motifs at MIT, Cambridge, USA)

MEME (Multiple EM for Motive Elicitation: Motive discovery at San Diego Supercomputer Centre, SDSC, Ca, USA)

 

eMotif-maker (Build motifs that describe protein families or superfamilies at Stanford University, USA)

Meta-MEME (Buid motif at San Diego Supercomputer Centre, SDSC, Ca, USA)

 

CDART (Conserved Domain Architecture Retrieval Tool at NCBI, USA)

SearchPfam at Wustl or EBI (Search a protein against Pfam domain/family database)

InterProScan (Search a protein against the integrated protein domains and functional sites database InterPro at EBI, UK)

CD-Search (Search a protein against conserved domain database CDD with RPS-BLAST at NCBI, USA)

COGnitor (Search a protein agains the COG database at NCBI)

iProClass Search (Search a protein against PIR's integrated protein class database at Georgetown 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)

ConSurf (Identification of functional regions in proteins by surface-mapping of phylogenetic information at Tel Aviv University, Israel)

 

ProDom (Automatically generated protein domain database at Toulouse, Fr)

Modules (Mobile protein domains database at EMBL)

SBASE (Protein domain library at ICGEB, Trieste, 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 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, computation and analysis of pathways

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

aMAZE (Query tools for metabolic and signal transduction pathway analysis at ULB, Belgium)

Protein-protein interactions

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

PreBIND (Locate biomolecular interaction information in the scientific literature at the Samuel Lunenfeld Research Institute, Canada)

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

BINDBLAST (Search BIND database with BLAST)

MINT (Molecular INTeraction database at Rome University, It)

GRID (General Repository of Interaction Datasets at the Samuel Lunenfeld Research Institute, Canada)

PPI viewer (Mammalian protein-protein interaction database and viewer at RIKEN, Japan)

STRING (database of predicted functional associations among genes/proteins at the EMBL)

InterPrets (Interaction prediction through structure at the EMBL)

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)

Artemis (Free (large-) DNA sequence viewer and annotation tool at the Sanger Institute, UK)

Gene Ontology tools (Universal function annotation vocabulary by the Gene Ontology Consortium )

Automatic alert for related new sequence

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)
New microbial Genomes Notification (Receive notifications by e-mail about new complete genomes in GenBank)

Multiple sequence alignment

 

ClustalW (Multiple sequence alignment at EBI, UK)

Multiple sequence alignment (at Baylor College of Medecine, 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)

ConSurf (Identification of functional regions in proteins by surface-mapping of fhylogenetic information at Tel Aviv University, Israel)

Links to phylogeny software tools and servers (at the University of Washington, USA)

 

Organism classification

NCBI Taxonomy

The Tree of Life Project

TreeBASE (database of phylogenetic knowledge hosted by the University at Buffalo, USA)

ArrayExpress (Repository for microarray data at EBI, UK)

GEO (Gene Exprssion Omnibus at NCBI)

SMD (Stanford microarray database, including microarray tools and tool links)

YMD (Yale microarray database)

Expression Profiler (Web-based microarray data analysis at EBI, UK)

GenMapp (Free computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes )

TBI Expression Analysis (Find differential genes between two filter hybridisation experiments at DFKZ, Heidelberg)

Other links to public microarray and gene expression databases

PubMed (Search public version of full Medline integrated in ENTREZ at NCBI, USA)

PubMed Central (Free online access to full text of life Science rechearch articles at NCBI, USA)

FreeMedicalJournals (Links to free online medical journals)

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)

Brutlag Bioinformatics Group (at Stanford University, USA)

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 (at IGH, Montpellier, Fr)

GenomeNet Japan

ISCB (International Society for Computational Biology)

ISREC (Swiss Institute for Experimental Cancer Research)

MBCR (Biomedical Computing Facility)

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)

RFCGR (MRC Rosalind Franklin Centre for Genomic Research, Hinxton, UK)

Roslin Institute Bioinformatics (Edinburg, UK)

Sanger Institute (Hinxton, UK)SBG (Structural Bioinformatics Group at the EMBL, Heidelberg, Germany)

SDSC (San Diego Supercomputer Center, USA)

SHGC (Stanford Human Genome Center)

SIB (Swiss Institute for Bioinformatics, Geneva, CH)

Stanford Genome Technology Center

Stanford Genomic Resources

TIGR (The Institute for Genomic Research, USA)

UCL Biochemistry BSM Group (Biomolecular Structure and Modelling Group, UK)

Washington Genome Sequencing Center

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Links to other collections of bioinformatics resources

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BioBencHelper

BIW (BioInformatics Web of Suresh Kumar)

BCM Search Launcher (Interface for related WWW tools at Baylor College of Medicine)

GenomeWeb (at the MRC RFCGR, Hinxton, UK)

HNB (Helmholz Network Network for Bioinformatics, Germany)

Luke's EMBOSS GUI (GUIs to EMBOSS, the European Molecular Biology Open Software Suite for sequence analysis)

AMOS' WWW Page Links (more than 1000 links listed by Amos Bairoch)

ExPASy Proteomics Tools (CH)

CMS Molecular Biology Resource (at San Diego Supercomupter Center, US)

Pack of WWW Tools for Molecular Analysis (at Adelaide University, Australia)

ABIM online Analysis Tools (Université Aix-Marseille, Fr)

Bioinformatics resources CCP11 (MRC, UK)

MolBiol.net (Links directory of bioinformatics, genomics, proteomics, biotechnology and molecular biology )

List of other Molecular Biology Resources

OMIA (Online Mendelian Inheritance in Animals, University of Sydney, Australia)

OMIM  (Online Mendelian Inheritance in Man at the NCBI)

The MERCK Manual of Diagnosis and Therapy  (Guide to clinical information)

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)

Logiciels (Software directory at Institut Pasteur with links to providers and tutorials)

Molscript

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

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NIST Standard Reference Data Products Catalog

ChemFinder

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Educational resources

[Back to Contents]

S-Star.org (Online Bioinformatics education by a collaboration of 7 universities wordwide)

BioComputing Hypertext Coursebook (Bielefeld, Germany)

Guide to Molecular Sequence Analysis (By Andrew Louka, University of Oslo, Norway)

NCBI Education (Bioinformatics definitions and tutorials at the NCBI, USA)

 

Molecules in the Classroom (UMass Amherst USA)

DNA Structure

NDB Biomolecular Resource (Nucleic Acid education)

NDB Atlas of Nucleic Acid Containing Structures

Teachers' Molecular Visualization Resources

BioMolecular Structure Education Web Sites

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)