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Oligonucleotide Properties Calculator

 

RNA & DNA Folding  Applications 

 

Bioinformatic Resources

 

Multiple sequence alignment by Florence Corpet

 

Biotech News Agbiotechnet BIO The BioInformatics Resource Bio Online BioSpace DOE EDGAR Genome Project News, ORNL HMS Beagle News & Events, NIH PhRMA Recombinant Capital Signals USDA What's New, American Society for Microbiology Biotech Directory of biotechnology and pharmaceutical companies

Bioinformatic Databases NCBI ENTREZ EXPASY PROSITE ENZYME SWISS-PROT SRS Sequence Retrieval System RDP Ribosomal Database Project II The Tree of Life The RNA World

Genome Centers SANGER TIGR PASTEUR JENA ORNL Oak Ridge National Laboratory Brookhaven National Lab Cold Spring Harbor Laboratory Genoscope GÉNÉTHON Goettingen Genomics Laboratory Lawrence Berkeley National Laboratory Los Alamos National Lab Max-Planck-Institute for Biochemistry, Germany MITI Kazusa DNA Research Institute Stanford University University of Oklahoma, Advanced Center for Genome Technology University of Pennsylvania Center for Bioinformatics University of Utah, Utah Genome Center University of Washington WA, Genome Center University of Wisconsin, Department of Bacteriology Whitehead Institute for Genome Research NCGR National Center for Genome Research NHGRI The National Human Genome Research Institute NIAID National Institute of Allergy and Infectious Diseases Home Cambridge Healthtech Institute Virtual Genome Center

Genome Databases GOLD 2.0 Genomes monitor page Human Genome News KEGG PEDANT

Metabolic Pathways KEGG Kyoto encyclopedia Soybean metabolic DB MPW the Metabolic Pathways Database The University of Minnesota Biocatalysis/Biodegradation Database The Main Metabolic Pathways on Internet BioNOME - Resources EMP Enzymes and Metabolic Pathways Biochemical Pathways, EXPASY

Motif Identification Pfam, Sanger Pfam, WU HMM, WU ProDom COGs Clusters of Orthologous Groups (NCBI) ScanProsite Protein against PROSITE MOTIF Searching Protein Sequence Motifs PROSCAN (PROSITE SCAN), PBIL France Helix-Turn-Helix motif prediction, PBIL France Blocks WWW Server multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins PRINTS Protein Motif Fingerprint Database OWL Database Protein Functional Analysis, BMERC Protein motifs, University of Minnesota DBMOTIF Search Protein Motifs in protein databases, University of Minnesota Sequence Scan search for a protein motif (3 to 30 residues) (MIPS) RAMdbP Retrieving patterns in protein databases

Phylogenetic Analysis Phylogeny: Phylip programs, Pasteur BIONJ: a version of the NJ algorithm improved for molecular sequences, Pasteur Puzzle:Tree reconstruction for sequences by quartet puzzling and maximum likelihood, Pasteur Phylogeny and Evolution, University of Oxford UK Taxonomy and Systematics, University of Glasgow (software) AVAILABLE PHYLOGENY PROGRAMS NJplot for parsimony, distance or maximum likelihood trees Unrooted Phylo_win for neighbor-joining, parsimony and maximum likelihood methods PHYLIP a package of programs for inferring phylogenies Molphy phylogenetic analysis with (ML) and (NJ) Phylogenetic Tree prediction Putative phylogenetic trees prediction for sequence multiple alignment by cluster and topological algorithms PAML Phylogenetic Analysis by Maximum Likelihood TreeView MacClade Phylogeny and Reconstructing Phylogenetic Trees TreeBase A Database of Phylogenetic Knowledge Phylogenetics Software Resources

Protein Domains ProDom protein domain database PROSITE Dictionary of protein sites and patterns The Protein Sequence Databases of BioBase

Sequence Alignments Multiple Sequence Alignments BOXSHADE 3.21 Pretty Printing and Shading of Multiple-Alignment files MultAlin Multiple sequence alignment by Florence Corpet CLUSTALW, PBIL France MULTALIN, PBIL France Multiple Alignment, DEAMBULUM Multiple Protein Sequence Analysis, PBIL France Consensus, the Bork group EMBL Tools for Alignment, the Bork group Divide-and-Conquer Multiple Sequence Alignment for high quality simultaneous multiple sequence alignments DIALIGN 2 especially suited to detect local similarities among distantly related sequences AliBee - Multiple Alignment ALIGN Compendium of Protein Sequence Alignments SeaView CINEMA Colour INteractive Editor for Multiple Alignments LalnView, PBIL France ToPLign implements standard pairwise and multiple alignment methods with flexible parameter handling Match-Box Web Server 1.2 multiple sequences alignment of proteins, Belgium VSNS BioComputing Division Multiple Alignment Resource Page AMAS Analyse Multiply Aligned Sequences, EBI MSAPBC Sequence Alignment and Comparison

Sequence Homology Search Engines BLAST, NCBI WU-BLAST2, EBI Fasta3, EBI FASTA Sequence Similarity Search Served by GenomeNet BLITZ Database Searches an automatic electronic mail server for the MPsrch program of Shane Sturrock and John Collins, Biocomputing Research Unit, University of Edinburgh, Scotland Homology and Similarity Searching (EBI)

Structure Protein Data Bank (PDB) CASP2, Sanger The Dali server comparing protein structures in 3D, EBI NDB Biological Structure Resource, Rutgers University PDBsum, UK SCOP Structural Classification of Proteins The PredictProtein server (EMBL) RasMol Home Page to display molecular structure PHD Predict Protein Secondary Structure EMBL-Heidelberg DICROPROT, PBIL France CATH Protein Structure Classification Antibody Structure and Sequence Information Garnier-Robson-Osguthorpe Secondary Structure Prediction NNPREDICT Protein Secondary Structure Prediction PREDATOR Protein secondary structure prediction from single sequence or a set of sequences (EMBL) TMAP multiple sequence alignment form Database of Macromolecular Movements Image Library of Biological Macromolecules, JENA Secondary structure prediction, PBIL France

Last update: Septembre 2005/ Guennadi Sezonov