L I N K S Genome Computing Resources NCSA Computational Biology Ghostscript, Ghostview and GSview CGG Genomic Analysis Web Tools Statistical Genetics Software (RHMAP etc.) European Bioinformatics Institute (EBI) EMBL Computational Services at EMBL-Heidelberg AA Analysis - Amino Acids Identification at EMBL-Heidelberg AA CompIdent - Protein Composition identification at ExPASy, Switzerland AA CompSim - Compare the Amino Acid Composition ExPASy, Switzerland AbCheck - Test an Antibody Sequence Against the Kabat Database at U. College-London, UK ALIGN - Optimal Global Alignment of Two Sequences with No Short-cuts at EERIE-Nimes, France and MIPS, Germany AllAll - Relationships in a Set of Related Peptides at ETH-Zürich, Switzerland AllAllDB - Search the All-Against-All Database of SwissProt at ETH-Zürich, Switzerland AMAS - Analysis of Protein Multiple Sequence Alignments at U. Oxford, UK ASC - Analytic Surface Calculation of PDB Protein Structures at EMBL-Heidelberg ATLAS - Search DNA and Protein Sequence Databases at MIPS, Germany BCM Search Launcher at Baylor College of Medicine BioTools Incorporated (BTI) BEAUTY - BLAST Enhanced Alignment Utility (see Documentation) at Baylor College of Medicine BERLIN - RNA Databank of 5S rRNA and 5S rRNA Gene Sequences at CAOS/CAMM, The Netherlands BIOACCELERATOR at Weizmann Institute of Science, Israel bioCUSI - Multiple Access to Biological Servers at OCMS-Oxford Biological Units - Expanded PDB Entries with Full Biological Units at Brookhaven National Laboratory Biologist's Search Palette - Collection of Search Engines for Biological Databases at Oxford U., UK BLAST - Basic Local Alignment Research Tool at NCBI BLASTPAT - BLAST-based Pattern Database Search (see Documentation) at Baylor College of Medicine BLITZ - Fast comparison of protein sequences against SwissProt (see Documentation) at EBI, UK BLOCKS - Database of Highly Conserved Regions in Proteins and BLOCKS-WAIS at Fred Hutchinson Cancer Research Center, BLOCKS at EMBL-Heidelberg BioMagResBank - A Database of NMR-Derived Protein Structures at BIMAS-NIH BioSCAN - Biological Sequence Comparative Analysis at U. North Caroline BMCD - Biological Macromolecule Crystallization Database at CARB BOXSHADE - Pretty Printing and Shading of Multiple-Sequence Alignments at ISREC, Switzerland CATH - Protein Structure Classification at UCL-London, UK CLUSTALW - Multiply Sequence Alignments at IBC-Washington U. Codon Usage - Analysis of Different ORFs in a Gene Sequence at U. Minnesota Coils - Prediction of Coiled Coil Regions in Protein Sequences at ISREC, Switzerland CpGIsle - CpG Islands Database at BEN, Belgium CuraTools - A collection of integrated bioinformatic tools customized into one interface. Darwin - Data Analysis and Retrieval With Indexed Nucleotide/Peptide Sequences at ETH-Zürich, Switzerland dbEST - Database of Expressed Sequence Tags at NCBI DBGET - Integrated Database Retrieval System (w/ diagram links) at GenomeNet, Japan DDBJ - DNA Database of Japan at National Institute of Genetics, Japan Dot Plot - Compare a DNA Sequence with Itself at U. Minnesota DrugBank - Three-dimensional Drug Structure Databank at NIH DSSP - Database of Secondary Structure of Proteins from PDB (see Documentation) at EMBL-Heidelberg EC Enzyme at Johns Hopkins and EC Number Table at G enomeNet, Japan and GenoBase Enzyme Index at NIH Ecoli Learning EMBL - Nucleotide Sequence Database and EMBL-New Entries at EMBnet -Basel EMNEW - Index of New EMBL Sequences at EBI, UK EMP Compound and EMP Pathways - Selkov Enzyme and Metabolic Pathway (EMP) Database at NIH EMP Metabolic Pathways - Navigation in Metabolic Pathways from MCS-Computational Biology at A rgonne National Laboratory ENTREZ - Protein and Nucleotide Database (see Documentation) at NCBI ENZYME - The Enzyme Data Bank at ExPASy, Switzerland Enzyme Structures Database - Structures of Enzymes Deposited in the PDB at UCL-London, UK EPD - Eucaryotic Promoter Database at EMBL-Heidelberg, Germany and EPD at GenomeNet, Japan EPO - European Patent Office Nucleotide Database at BiO/U. Oslo, Norway and EPO at CSC, Finland The EST Figure-Outer - The EST BLAST servers along with two routes to Entrez FASTA - Compare a Nucleic Acid Sequence to Nucleotide Sequence Databases (w/ updates) at EBI, UK, FASTA (Berlin, Vectorbank, etc) at Stanford U., FASTA at EERIE-Nimes, France and FASTA at CRIHAN, France FASTPAT - FASTA-based Pattern Database Search (see Documentation) at Baylor College of Medicine FlyBase - Genetic and Molecular Database for Drosophila at Harvard U. FSSP - Database of Families of Structurally Similar Proteins derived from PDB at EMBL-Heidelberg FTHOM - Compare Protein Domain Homology at ABC, Hungary GDB - Human Genome Data Base at Johns Hopkins GenBank Database (+Updates) at NCBI and GenBank-Fetch at Washingto n U. Gene Finder - Predict Gene Structure, Internal Exons and Splicing Sites in DNA and Exon-Exon Junstion in cDNA at Baylor College of Medicine GenLang - Find Genes and Other Higher-Order Features in Nucleotide Sequences at CBIL-U. Pennsylvania GenoBase at NIH Genome Databases and Genome Centers - World Wide Links at EERIE-Nimes, France Genome Workstation - Genome Related Links at Roslin Institute, UK Genomic Maps - Links to Genome Specific Resources at Biotech-Indiana GenQuest - Search Against Protein Databases with the Q server at Johns Hopkins Grail - Analysis of the Protein Coding Potential of a DNA Sequence (see Documentation) at ORNL GSDB - Genome Sequence Database at NCGR GuessProt - Selects SwissProt proteins given pI and Mw at ExPASy, Switzerland HHS - SwissProt and PDB Systematic Sequence Classification Database at Washington U. HOVERGEN - Database of Homologous Vertebrate Genes at CAOS/CAMM, The Netherlands HPT - Protein Sequence Pattern Recognition in the PIR Database and HPT-Homology at MIPS, Germany HSSP - Database of Homology-Derived Structures of Proteins based on PDB and SwissProt at EMBL-Heidelberg Kabat - Database of Proteins of Immunological Interest at Johns Hopkins Kinemage-Index - "Kinetical Images" by Protein Type at Protein Science Klotho - Biochemical Compounds Declarative Database at Washington U. LALIGN - Calculates the N-Best Local Alignments Between Two Sequences at EERIE-Nimes, France LFASTA - Local Similarity Searches Between Two Sequences Showing Local Alignments at EERIE-Nimes, France LIGAND - Ligand Chemical Database for Enzyme Reactions at GenomeNet, Japan LiMB - Listing of Molecular Biology Databases at NIH and LiMB at EMBL-Heidelberg MassSearch - Search SwissProt or EMBL Databases by Protein Mass After Digestion at ETH-Zürich, Switzerland Metabolic Database - Metabolic Reactions and Pathways at CGSC-Yale U. and Metabolic Database at INRA-Moulon, France MGD - Mouse Genome Database at Jackson Laboratory MHCPEP - Database of Major Histocompatibility Complex (MHC) Binding Peptides at WEHI-Melbourne, Australia MIPS-Alert - Automated Sequence Information Queries at MIPS, Germany Molecules R US - Interactive Text and Images of PDB Files at NIH MPBD - Molecular Probe Data Base at EMBL-Heidelberg and MPDB at U. Agricultural Sciences, Sweden MOOSE - Macromolecular Object Oriented Search Engine to Extract PDB Contained Information at Columbia U. MSA - Multiple Sequence Alignment at Washington U. MOTIF - Search Patterns in Protein Sequences at GenomeNet, Japan Motif at GenomeNet, Japan w/ search from Iowa State Multiple Sequence Alignments - CLUSTAL-W, MAP, and PIMA alignments at Baylor College of Medicine NDB - Nucleic Acid Database at Rutgers U. nnPredict - Predict Protein Secondary Structure at UCSF and nnPredict at w/ search from Iowa State NRL_3D - Sequence/Structure Database derived from PDB at Johns Hopkins and NRL_3D at EMBL-Heidelberg NRSub - A Non-Redundant DNA Sequence Database for Bacillus subtilis at National Institute of Genetics, Japan NuclPepSearch - Search SwissProt for a Nucletide Sequence at ETH-Zürich, Switzerland NYC-MASS - Protein Mass Spectrometry Database at Rockefeller U. OBSTRUCT - Correlate Sequence Subsets of PDB Protein Structures at EMBL-Heidelberg OMIM - Online Mendelian Inheritance in Man at Johns Hopkins Organelle Genome - A Sequence Database at U. Montreal Organisms and Strains - Links to Databases Specific to Organism and Cell Collections at Biotech-Indiana OWL - Non-Redundant Protein Sequence Database (Updated Daily) at Johns Hopkins and OWL at UCL-London, UK PatScan - Look for Pattern Matches in DNA or Protein Sequences at Argonne National Laboratory PatternFind - Search the SwissProt and Genpept Protein Sequence Databases with a PROSITE-formatted Pattern at ISREC, Switzerland PDD - Protein Disease Database at NIMH-NCI PDB-Browser, PDB-Index and PDB-Pending - Protein Data Bank Structures at Brookhaven National Laboratory, PDB at GenomeNet Japan PDB at U. Genova, Italy, PDB-List and PDB-Annotated at Brussels Free U., Belgium and PDB-Select at EMBL-Heidelberg PDB At A Glance - Hierarchic Access to PDB Files at NIH PDBFINDER - A Database Containing PDB, DSSP and HSSP Information (see Documentat ion) at EMBL-Heidelberg PDBSTR - Re-organized Protein Data Bank at GenomeNet, Japan PepPepSearch - Search SwissProt for a Peptide Sequence at ETH-Zürich, Switzerland Plant EST Analysis - Similarity Analysis of Different Plant cDNA/EST Sequences at U. Minnesota PHD - Predict Protein Secondary Structure at EMBL-Heidelberg w/ search from Iowa Stat e PHILIP-Bootstrapping Analysis - Divergence Between Protein or Nucleotide Sequences at Institut Pasteur, France Phospepsort - Digest Phosphorylated Peptide Sequences at EERIE-Nimes, France pI/Mw - Compute the Theoretical pI and Molecular Weight of a Protein Sequence at ExPASy, Switzerland PIR - Protein Identification Resource Database at Johns Hopkins PIRALN - Database of Sequence Alignments based on PIR at EMBL-Heidelberg PMD - Protein Mutant Database at GenomeNet, Japan and PMD at EMBL-Heidelberg PMOTIF - Search Protein Motifs in Gene Sequence at U. Minnesota Poland - Calculate the Thermal Denaturation Profile of Double Stranded RNA or DNA at Uni-Düsseldorf, Germany PredictProtein - Predict Protein Secondary Structure at EMBL-Heidelberg PRF - Protein Research Foundation Sequence Database at GenomeNet, Japan Primer - Select PCR Primers in a Gene Sequence at WICGR-MIT and Primer at U. Minnesota PRINTS - Protein Motif Fingerprints Database (see Documentation) and PRINTS-ALIGN at UCL-London, UK and PRINTS at EMBnet-Basel, Switzerland ProDom - A Protein Domain Database and ProDom-Search at INRA-Toulouse, France, ProDom and ProDom-Search at Sanger Centre, UK and ProDom at EMBL-Heidelberg ProfileScan - Search a Sequence Against a Library of Profiles at ISREC, Switzerland ProLink - Integrated Database of Protein Structure, Sequence Homology, and Functional Pattern Information at BMERC PROPSEARCH - Protein Sequence Search for Structural Homology Based on Aminoacid Properties at EMBL-Heidelberg PROSITE - Protein Sites and Patterns Database at ExPASy, Switzerland, PrositeScan at ISREC, Switzerland and PROSITE-Search at EMBL-Heidelberg Protein-Extras at EMBL-Heidelberg Protein Families - Links to Information on Different Protein Families at Iowa State Prot-ID - Identify a Protein from Masses of Enzymatic Digestion Peptide Fragments at Rockefeller U. Protein Motions - DataBase of Protein Movements at Stanford U. PROWL - Multiple Analysis of Protein/ Amino Acid Sequence at Rockefeller U. PSA - Protein Sequence Analysis for Sequences of Unknown Structure at BMERC/MBCRR PSORT - Predict Protein Sorting Signals Coded in Amino Acid Sequences at GenomeNet, Japan PSSP - Protein Secondary Structure Prediction at Baylor College of Medicine PUMA - Phylogeny of Unicellular Organims with Metabolism and Alignments from MCS-Computational Biology at Argonne National Laboratory PUU - Protein Domains Database Based on PDB-Select at EMBL-Heidelberg RDP - Ribosomal Database Project at U. Illinois ReBase - Restriction Enzyme Database and ReBase-Search at New England Biolabs, ReBase at EMBL-Heidelberg and ReBase at Johns H opkins REPRO - Recognition of Protein Sequence Repeats at EMBL-Heidelberg RNA Secondary Structures - Information on Group I Introns and rRNA at U. Colorado-Boulder rRNA - Databases of Ribosomal Subunit RNA Sequences at U. Antwerp, Belgium RSVP - Rapid Sequence Visualization in Postscript for Analysis of DNA Sequences at CBIL-U. Pennsylvania SAPS - Statistical Analysis of Protein Sequences at ISREC, Switzerland SBASE - Library of Protein Domains and SBASE-Search > at ICGEB-Trieste, Italy SCANPS - Scan Protein Sequences at U. Oxford, UK SCOP - Structural Classification of Proteins at Cambridge, UK and SCOP at U. South Florida Sequence Annotation - Annotations on NCBI Sequences at Baylor College of Medicine Sequence Translation - Translate Gene Sequences at U. Minnesota Sleuth - Amino Acid Conformation and Solvent Accessibility of PDB Files at Washington U. SOPM - Self Optimized Prediction Method for Prediction of Protein Secondary Structure at IBCP-CNRS, France SRSWWW - Network Browser for Databanks in Molecular Biology (w/ diagram links) at EMBL-Heidelberg SRSWWW-Directory - Directory of SRSWWW Network Browsers for Biological Databanks and SRSWWW-Global Status at EMBnet-Basel SSEARCH - Universal Sequence Comparison Using the Smith-Waterman Algorithm at EERIE-Nimes, France SSPRED - Predict the Secondary Structure of Proteins at EMBL-Heidelberg, Germany STRIDE - Find Secondary Structural Elements in PDB Proteins Structures at EMBL-Heidelberg STS Pipeline - Analysis and STS Primer Picking of Short DNA Sequences with Duplicate Checking, Sequence Repeat Finding, Restriction Analysis, Vector Identification and BLAST Searching at MIT SURVOL - Analysis of Protein Atomic Volumes at UCMB, Belgium Swiss-2DPage - Two-dimensional Polyacrylamide Gel Electrophoresis Database at ExPASy, Switzerland SWISSDOM - SwissProt Entries in a ProDom Map at EBI, UK Swiss-Model > - Automated Protein Modelling at ExPASy, Switzerland SWISSNEW - New SwissProt Sequences at EBI, UK SwissProt - Protein Sequence Database (+ Weekly Updates) at ExPASy, Switzerland Swiss-Shop > - Automated SwissProt and Prosite Information Queries at ExPASy, Switzerland TBASE - Transgenic/Targeted Mutation Database at Johns Hopkins TFASTA - Match a Protein Sequence Against All Six Frames of GenBank Sequences at EERIE-Nimes, France TFD - Transcription Factor Database at NIH TFFACTOR and TFSITE - Transcription Factor Data at EMBL-Heidelberg Tm - Oligonucleotide Melting Point Determination at U. Minnesota TMAP - Identification of Transmembrane Segments on a Protein Sequence at EMBL-Heidelberg TMBASE - Transmembrane Protein Database at U. Lausanne, Switzerland TMpred - Prediction of Transmembrane Regions and Orientation in Protein Sequencs at ISREC, Switzerland Translate - Translate a Nucleotide Sequence to a Protein at ExPASy, Switzerland and Translate at EBI, UK TreeGen - Tree Generation from Distance Data at ETH-Zürich, Switzerland TREE-PUZZLE - Maximum likelihood analysis for nucleotide, amino acid, and two-state data by Korbinian Strimmer and Arndt von Haeseler TREMBL - Database of Translated Peptide Sequences of All CDS Features from EMBL Sequences at EMBL-Heidelberg VecBase - Cloning Vector Sequence Database.at CAOS/CAMM, The Netherlands Vector-DB - Cloning Vector Database at Queen's U.-Kensington, Canada , VECTOR at BEN, Belgium , Vector at Johns Hopkins and Vector-ig a t IVR, Kyoto-U., Japan VisAlign - The Alignment Color Viewer to Color 2 Aligned Amino Acid Sequences by Hydrophobicity at EBI, UK VisProt - The Protein Colorer to Color Amino Acid Sequences by Hydrophobicity at EBI, UK WebGene - ORF and protein analysis | Restriction Enzyme Analysis by Tongjia Yin WebLogo - Sequence Logo Generation at Cambridge U., UK ZPRED - MultPredict Secondary Structure of Multiply Aligned Protein Sequences at Ludwig Institute for Cancer Research, UK

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