BIOTECH NEWS Agbiotechnet BIO The BioInformatics Resource Bio Online BioSpace Biotechnology Patents DOE EDGAR Genome Project News @ ORNL HMS Beagle Law Journal Extra News & Events @ NIH PhRMA Recombinant Capital The Scientist Signals USDA What's New @ American Society for Microbiology

BIOINFORMATIC DATABASES NCBI ENTREZ EXPASY PROSITE ENZYME SWISS-PROT SRS Sequence Retrieval System RDP Ribosomal Database Project II The Tree of Life American Society for Microbiology The RNA World

GENOME CENTERS SANGER TIGR PASTEUR JENA ORNL Oak Ridge National Laboratory Baylor College of Medicine @Houston, TX Brookhaven National Lab Cold Spring Harbor Laboratory Genoscope GÉNÉTHON Goettingen Genomics Laboratory Lawrence Berkeley National Laboratory Los Alamos National Lab McDermott Center for Human Growth and Development Max-Planck-Institute for Biochemistry @Germany MITI Kazusa DNA Research Institute Pasteur Institute Sanger Center Stanford University University of Oklahoma University of Pennsylvania Center for Bioinformatics University of Utah University of Washington @Seattle WA University of Wisconsin Washington University @St. Louis, MO Whitehead Institute for Genome Research Research JENA NCGR National Center for Genome Research NHGRI The National Human Genome Research Institute NIAID National Institute of Allergy and Infectious Diseases Home Page Cambridge Healthtech Institute

GENOME DATABASES GOLD 1.0 Genomes monitor page Microbial Genomics News GeneQuiz @EBI KEGG PEDANT

METABOLIC PATHWAYS KEGG Kyoto encyclopedia Soybean metabolic DB Drosophila melanogaster pathways MPW the Metabolic Pathways Database The University of Minnesota Biocatalysis/Biodegradation Database Klotho: Biochemical Compounds Declarative Database The Main Metabolic Pathways on Internet GENETIC NETWORKS DYNAMICS - METABOLIC PATHWAYS EMP Enzymes and Metabolic Pathways Biochemical Pathways @EXPASY

SEQUENCE HOMOLOGY SEARCH ENGINES PSI_BLAST @NCBI BLAST2 gapped allignment @NCBI BLAST search page @NCBI WU-BLAST2 @EBI Fasta3 @EBI FASTA Sequence Similarity Search Served by GenomeNet TFASTA Match a Protein Sequence Against All Six Frames of GenBank Sequences @EERIE-Nimes, France 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 Sequence similarity searches (@EBI) GenQuest for FASTA and BLAST of a protein sequence GeneFIND Family Identification System @Univ of Texas

SEQUENCE ALIGNMENTS ClustalW Multiple Sequence Alignment (@BCM) 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 at the Bork group BCM Search Launcher for Multiple Sequence Alignments 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 GeneDoc A Full Featured Multiple Sequence Alignment Editor and Shading Utility with Phylogenetic Tree Support Multiple Alignment Multiple Alignment Resource Page ALIGN Compendium of Protein Sequence Alignments SeaView CINEMA Colour INteractive Editor for Multiple Alignments LALNVIEW graphical program for visualizing local alignments between two sequences LalnView @PBIL GeneDoc Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows The Multiple Alignment Sequence Editor Bio-lirmm / Map123d for protein homology modelling 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 MSA Multiple Sequence Alignment @Washington U.

MOTIF IDENTIFICATION Pfam @Sanger HMM search in Pfam-A @Sanger Pfam @WU HMM @WU Prodom THE MEME SYSTEM COGsClusters of Orthologous Groups (@NCBI) ScanProsite Protein against PROSITE BCM Search Launcher BLOCK MAKER MOTIF Searching Protein Sequence Motifs Prosite search @PBIL, France Pattern search @PBIL, France BIOCCELERATOR @EMBL BCM Search Launcher General Protein Sequence/Pattern Searches @Human Genome Center, Baylor College Blocks WWW Server multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins PRINTS Protein Motif Fingerprint Database FPAT searching Protein Databases with a Regular Expression Regular Expression Searches of the OWL Database Protein Functional Analysis at BMERC HSSP protein structure-sewquence alignments and family profiles db Protein motifs @U. Minnesota DBMOTIF Search Protein Motifs in protein databases @U. Minnesota PMOTIF Search Protein Motifs in Gene Sequence @U. Minnesota Sequence Scan search for a protein motif (3 to 30 residues) (MIPS) RAMdbP Retrieving patterns in protein databases Amino Acids Frequencies @PBIL, France Helix-Turn-Helix motif prediction @PBIL, France PATSCAN pattern matcher @Bari, Italy

PROTEIN DOMAINS ProDom protein domain database Multicoil predicts the location of coiled-coil regions Paircoils predict the location of coiled-coil regions PROSITE Dictionary of protein sites and patterns FTHOM Compare Protein Domain Homology at ABC, Hungary HOMOL @MIPS

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 CMSMBR Molcecular Evolution Phylogeny-links Introduction to Phylogeny Phylogeny and Evolution @Univ of Oxford, UK Taxonomy and Systematics @Univ of Glasgow (software) The Bioinformatics Resource software @Stanford 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 DARWIN (Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences) Molphy phylogenetic analysis with (ML) and (NJ) PUZZLE Tree reconstruction for sequences by quartet puzzling and maximum likelihood Phylogenetic Tree prediction Putative phylogenetic trees prediction for sequence multiple alignment by cluster and topological algorithms PAML Phylogenetic Analysis by Maximum Likelihood TreeGen Tree generation from distance data @ETH-Zürich, Switzerland TreeView RAPDistance MacClade COMPARE 2.0 Computer programs for the phylogenetic analysis of comparative data CAIC comparative analysis package for the Apple Macintosh Evolutionary Comparisons using Dst Phylogeny and Reconstructing Phylogenetic Trees RDP Ribosomal Database Project @UIUC TreeBase A Database of Phylogenetic Knowledge Phylogenetics Software Resources

STRUCTURE PDB @Brookhaven National Laboratory CASP2 @Sanger The Dali server comparing protein structures in 3D @EBI NDB Biological Structure Resource @Rutgers Univ PDBsum @UK Protein Secondary Structure Prediction @BCM Search Launcher SCOP Structural Classification of Proteins Macromolecular Structures @EBI CATH Protein Structure Classification Helical Wheel with Java The PredictProtein server (@EMBL) RasMol Home Page to display molecular structure PHD Predict Protein Secondary Structure @EMBL-Heidelberg PREDICTION of COIL-COIL @PBIL, France DICROPROT @PBIL, France Protein Secondary Structure Prediction via BCM Search Launcher Macromolecular Structure Query MOOSE: Macromolecular Object Oriented Search Engine permits querying structural database(s) CATH Protein Structure Classification Antibody Structure and Sequence Information Garnier-Robson-Osguthorpe Secondary Structure Prediction NNPREDICT Protein Secondary Structure Prediction Protein Structural Analysis at BMERC PREDATOR Protein secondary structure prediction from single sequence or a set of sequences (@EMBL) TMAP A service predicting transmembrane segments in proteins (@EMBL) BCM Search Launcher Protein Secondary Structure Prediction Protein Motions Database Image Library of Biological Macromolecules @JENA Secondary structure prediction @PBIL, France