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Part 1: Molecular Biology Search and Analysis

3D-ALI - Database relating Proteins Structures and Sequences (see Documentation) at EMBL-Heidelberg 
 AA Analysis  - Protein Identification in SwissProt and PIR using Amino Acid Composition at EMBL-Heidelberg  
 AA CompIdent - Protein Identification in SwissProt using Amino Acid Composition at ExPASy, Switzerland  
 AA CompSim - Compare the Amino Acid Composition of a SwissProt Entry with Other Entries at ExPASy, Switzerland  
 AA Sequence Analysis - Multiple Analysis of a Native or Modified Amino Acid Sequence at Rockefeller U.  
 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 Align at 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 
 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 

 - 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, BLAST (hiv, vector, etc) at Stanford U.
BLAST at GenomeNet, Japan, 
BLAST at EERIE-Nimes, France, 
BLAST at CRIHAN, France BLAST (with Entrez and SRS Links) at Baylor College of Medicine and 
BLAST at EPFL, Switzerland 

 BLASTPAT - BLAST-based Pattern Database Search (see Documentation) at Baylor College of Medicine 

 BLITZ (see Documentation) at EMBL-Heidelberg and BLITZ at EBI, UK 

 BLOCKS - Database of Highly Conserved Regions in Proteins  and BLOCKS-WAIS  at Fred Hutchinson Cancer Research Center
BLOCKS at EMBL-Heidelberg and 
BLOCKS-Search w/ search from Iowa State 

 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 

 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 GenomeNet, Japan and GenoBase Enzyme Index at NIH 

 ECDC - E. coli Database Collection at Uni-Gießen, Germany 

 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 Argonne 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 

 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 Washington U. 

 Gene Finder - Predict Gene Structure, Internal Exons and Splicing Sites in DNA and Exon-Exon Junstion in cDNA at

 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 Documentation) 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 State 

 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. 

 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

 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 Hopkins 

 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

 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 

 TreeGen - Tree Generation from Distance Data at ETH-Zürich, Switzerland 

 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 at IVR, Kyoto-U., Japan 

 WebLogo - Sequence Logo Generation at Cambridge U., UK 

 ZPRED - MultPredict Secondary Structure of Multiply Aligned Protein Sequences at Ludwig Institute for Cancer Research, UK