Part 1: Molecular Biology Search and Analysis
- 3D-ALI - Database relating Proteins Structures and Sequences (see Documentation) at EMBL-Heidelberg W3
- AA Analysis - Protein Identification in SwissProt and PIR using Amino Acid Composition at EMBL-Heidelberg W3
- AA CompIdent - Protein Identification in SwissProt using Amino Acid Composition at ExPASy, Switzerland W3
- AA CompSim - Compare the Amino Acid Composition of a SwissProt Entry with Other Entries at ExPASy, Switzerland W3
- AA Sequence Analysis - Multiple Analysis of a Native or Modified Amino Acid Sequence at Rockefeller U. W3
- AbCheck - Test an Antibody Sequence Against the Kabat Database at U. College-London, UK W3
- ALIGN - Optimal Global Alignment of Two Sequences with No Short-cuts at EERIE-Nimes, France and Align at MIPS, Germany W3
- AllAll - Relationships in a Set of Related Peptides at ETH-Zürich, Switzerland W3
- AllAllDB - Search the All-Against-All Database of SwissProt at ETH-Zürich, Switzerland W3
- AMAS - Analysis of Protein Multiple Sequence Alignments at U. Oxford, UK W3
- ASC - Analytic Surface Calculation of PDB Protein Structures at EMBL-Heidelberg W3
- ATLAS - Search DNA and Protein Sequence Databases at MIPS, Germany W3
- BCM Search Launcher at Baylor College of Medicine W3
- BEAUTY - BLAST Enhanced Alignment Utility (see Documentation) at Baylor College of Medicine W3
- BERLIN - RNA Databank of 5S rRNA and 5S rRNA Gene Sequences at CAOS/CAMM, The Netherlands W3
- BIOACCELERATOR at Weizmann Institute of Science, Israel W3
- bioCUSI - Multiple Access to Biological Servers at OCMS-Oxford W3
- Biological Units - Expanded PDB Entries with Full Biological Units at Brookhaven National Laboratory FTP
- Biologist's Search Palette - Collection of Search Engines for Biological Databases at Oxford U., UK W3
- 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 W3
- BLASTPAT - BLAST-based Pattern Database Search (see Documentation) at Baylor College of Medicine W3
- BLITZ - Fast comparison of protein sequences against SwissProt (see Documentation) at EBI, UK W3
- BLOCKS - Database of Highly Conserved Regions in Proteins W3 and BLOCKS-WAIS Gopher at Fred Hutchinson Cancer Research Center, BLOCKS at EMBL-Heidelberg W3
- BioMagResBank - A Database of NMR-Derived Protein Structures at BIMAS-NIH W3
- BioSCAN - Biological Sequence Comparative Analysis at U. North Caroline W3
- BMCD - Biological Macromolecule Crystallization Database at CARB W3
- BOXSHADE - Pretty Printing and Shading of Multiple-Sequence Alignments at ISREC, Switzerland W3
- CATH - Protein Structure Classification at UCL-London, UK W3
- CLUSTALW - Multiply Sequence Alignments at IBC-Washington U. W3
- Codon Usage - Analysis of Different ORFs in a Gene Sequence at U. Minnesota W3
- Coils - Prediction of Coiled Coil Regions in Protein Sequences at ISREC, Switzerland W3
- CpGIsle - CpG Islands Database at BEN, Belgium W3
- Darwin - Data Analysis and Retrieval With Indexed Nucleotide/Peptide Sequences at ETH-Zürich, Switzerland W3
- dbEST - Database of Expressed Sequence Tags at NCBI W3
- DBGET - Integrated Database Retrieval System (w/ diagram links) at GenomeNet, Japan W3
- DDBJ - DNA Database of Japan at National Institute of Genetics, Japan Gopher
- Dot Plot - Compare a DNA Sequence with Itself at U. Minnesota W3
- DrugBank - Three-dimensional Drug Structure Databank at NIH W3
- DSSP - Database of Secondary Structure of Proteins from PDB (see Documentation) at EMBL-Heidelberg W3
- EC Enzyme at Johns Hopkins and EC Number Table at GenomeNet, Japan and GenoBase Enzyme Index at NIH W3
- ECDC - E. coli Database Collection at Uni-Gießen, Germany W3
- EMBL - Nucleotide Sequence Database and EMBL-New Entries at EMBnet-Basel Gopher
- EMNEW - Index of New EMBL Sequences at EBI, UK W3
- EMP Compound and EMP Pathways - Selkov Enzyme and Metabolic Pathway (EMP) Database at NIH W3
- EMP Metabolic Pathways - Navigation in Metabolic Pathways from MCS-Computational Biology at Argonne National Laboratory W3
- ENTREZ - Protein and Nucleotide Database (see Documentation) at NCBI W3
- ENZYME - The Enzyme Data Bank at ExPASy, Switzerland W3
- Enzyme Structures Database - Structures of Enzymes Deposited in the PDB at UCL-London, UK W3
- EPD - Eucaryotic Promoter Database at EMBL-Heidelberg, Germany and EPD at GenomeNet, Japan W3
- EPO - European Patent Office Nucleotide Database at BiO/U. Oslo, Norway W3 and EPO at CSC, Finland Gopher
- 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 W3
- FASTPAT - FASTA-based Pattern Database Search (see Documentation) at Baylor College of Medicine W3
- FlyBase - Genetic and Molecular Database for Drosophila at Harvard U. W3
- FSSP - Database of Families of Structurally Similar Proteins derived from PDB at EMBL-Heidelberg W3
- FTHOM - Compare Protein Domain Homology at ABC, Hungary W3
- GDB - Human Genome Data Base at Johns Hopkins W3
- GenBank Database (+Updates) at NCBI and GenBank-Fetch at Washington U. W3
- Gene Finder - Predict Gene Structure, Internal Exons and Splicing Sites in DNA and Exon-Exon Junstion in cDNA at Baylor College of Medicine W3
- GenLang - Find Genes and Other Higher-Order Features in Nucleotide Sequences at CBIL-U. Pennsylvania W3
- GenoBase at NIH W3
- Genome Databases and Genome Centers - World Wide Links at EERIE-Nimes, France W3
- Genome Workstation - Genome Related Links at Roslin Institute, UK W3
- Genomic Maps - Links to Genome Specific Resources at Biotech-Indiana W3
- GenQuest - Search Against Protein Databases with the Q server at Johns Hopkins W3
- Grail - Analysis of the Protein Coding Potential of a DNA Sequence (see Documentation) at ORNL W3
- GSDB - Genome Sequence Database at NCGR W3
- GuessProt - Selects SwissProt proteins given pI and Mw at ExPASy, Switzerland W3
- HHS - SwissProt and PDB Systematic Sequence Classification Database at Washington U. W3
- HOVERGEN - Database of Homologous Vertebrate Genes at CAOS/CAMM, The Netherlands W3
- HPT - Protein Sequence Pattern Recognition in the PIR Database and HPT-Homology at MIPS, Germany W3
- HSSP - Database of Homology-Derived Structures of Proteins based on PDB and SwissProt at EMBL-Heidelberg W3
- Kabat - Database of Proteins of Immunological Interest at Johns Hopkins Gopher
- Kinemage-Index - "Kinetical Images" by Protein Type at Protein Science W3
- Klotho - Biochemical Compounds Declarative Database at Washington U. W3
- LALIGN - Calculates the N-Best Local Alignments Between Two Sequences at EERIE-Nimes, France W3
- LFASTA - Local Similarity Searches Between Two Sequences Showing Local Alignments at EERIE-Nimes, France W3
- LIGAND - Ligand Chemical Database for Enzyme Reactions at GenomeNet, Japan W3
- LiMB - Listing of Molecular Biology Databases at NIH Gopher and LiMB at EMBL-Heidelberg W3
- MassSearch - Search SwissProt or EMBL Databases by Protein Mass After Digestion at ETH-Zürich, Switzerland W3
- Metabolic Database - Metabolic Reactions and Pathways at CGSC-Yale U. and Metabolic Database at INRA-Moulon, France W3
- MGD - Mouse Genome Database at Jackson Laboratory W3
- MHCPEP - Database of Major Histocompatibility Complex (MHC) Binding Peptides at WEHI-Melbourne, Australia Gopher
- MIPS-Alert - Automated Sequence Information Queries at MIPS, Germany W3
- Molecules R US - Interactive Text and Images of PDB Files at NIH W3
- MPBD - Molecular Probe Data Base at EMBL-Heidelberg W3 and MPDB at U. Agricultural Sciences, Sweden Gopher
- MOOSE - Macromolecular Object Oriented Search Engine to Extract PDB Contained Information at Columbia U. W3
- MSA - Multiple Sequence Alignment at Washington U. W3
- MOTIF - Search Patterns in Protein Sequences at GenomeNet, Japan Motif at GenomeNet, Japan w/ search from Iowa State W3
- Multiple Sequence Alignments - CLUSTAL-W, MAP, and PIMA alignments at Baylor College of Medicine W3
- NDB - Nucleic Acid Database at Rutgers U. W3
- nnPredict - Predict Protein Secondary Structure at UCSF and nnPredict at w/ search from Iowa State W3
- NRL_3D - Sequence/Structure Database derived from PDB at Johns Hopkins and NRL_3D at EMBL-Heidelberg W3
- NRSub - A Non-Redundant DNA Sequence Database for Bacillus subtilis at National Institute of Genetics, Japan W3
- NuclPepSearch - Search SwissProt for a Nucletide Sequence at ETH-Zürich, Switzerland W3
- NYC-MASS - Protein Mass Spectrometry Database at Rockefeller U. W3
- OBSTRUCT - Correlate Sequence Subsets of PDB Protein Structures at EMBL-Heidelberg W3
- OMIM - Online Mendelian Inheritance in Man at Johns Hopkins W3
- Organelle Genome - A Sequence Database at U. Montreal Gopher
- Organisms and Strains - Links to Databases Specific to Organism and Cell Collections at Biotech-Indiana W3
- OWL - Non-Redundant Protein Sequence Database (Updated Daily) at Johns Hopkins and OWL at UCL-London, UK W3
- PatScan - Look for Pattern Matches in DNA or Protein Sequences at Argonne National Laboratory W3
- PatternFind - Search the SwissProt and Genpept Protein Sequence Databases with a PROSITE-formatted Pattern at ISREC, Switzerland W3
- PDD - Protein Disease Database at NIMH-NCI W3
- 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 W3
- PDB At A Glance - Hierarchic Access to PDB Files at NIH W3
- PDBFINDER - A Database Containing PDB, DSSP and HSSP Information (see Documentation) at EMBL-Heidelberg W3
- PDBSTR - Re-organized Protein Data Bank at GenomeNet, Japan W3
- PepPepSearch - Search SwissProt for a Peptide Sequence at ETH-Zürich, Switzerland W3
- Plant EST Analysis - Similarity Analysis of Different Plant cDNA/EST Sequences at U. Minnesota W3
- PHD - Predict Protein Secondary Structure at EMBL-Heidelberg w/ search from Iowa State W3
- PHILIP-Bootstrapping Analysis - Divergence Between Protein or Nucleotide Sequences at Institut Pasteur, France W3
- Phospepsort - Digest Phosphorylated Peptide Sequences at EERIE-Nimes, France W3
- pI/Mw - Compute the Theoretical pI and Molecular Weight of a Protein Sequence at ExPASy, Switzerland W3
- PIR - Protein Identification Resource Database at Johns Hopkins W3
- PIRALN - Database of Sequence Alignments based on PIR at EMBL-Heidelberg W3
- PMD - Protein Mutant Database at GenomeNet, Japan and PMD at EMBL-Heidelberg W3
- PMOTIF - Search Protein Motifs in Gene Sequence at U. Minnesota W3
- Poland - Calculate the Thermal Denaturation Profile of Double Stranded RNA or DNA at Uni-Düsseldorf, Germany W3
- PredictProtein - Predict Protein Secondary Structure at EMBL-Heidelberg W3
- PRF - Protein Research Foundation Sequence Database at GenomeNet, Japan W3
- Primer - Select PCR Primers in a Gene Sequence at WICGR-MIT and Primer at U. Minnesota W3
- PRINTS - Protein Motif Fingerprints Database (see Documentation) and PRINTS-ALIGN at UCL-London, UK and PRINTS at EMBnet-Basel, Switzerland W3
- 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 W3
- 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 W3
- PROSITE - Protein Sites and Patterns Database at ExPASy, Switzerland, PrositeScan at ISREC, Switzerland and PROSITE-Search at EMBL-Heidelberg W3
- Protein-Extras at EMBL-Heidelberg FTP
- Protein Families - Links to Information on Different Protein Families at Iowa State W3
- Prot-ID - Identify a Protein from Masses of Enzymatic Digestion Peptide Fragments at Rockefeller U. W3
- Protein Motions - DataBase of Protein Movements at Stanford U. W3
- PSA - Protein Sequence Analysis for Sequences of Unknown Structure at BMERC/MBCRR W3
- PSORT - Predict Protein Sorting Signals Coded in Amino Acid Sequences at GenomeNet, Japan W3
- PSSP - Protein Secondary Structure Prediction at Baylor College of Medicine W3
- PUMA - Phylogeny of Unicellular Organims with Metabolism and Alignments from MCS-Computational Biology at Argonne National Laboratory W3
- PUU - Protein Domains Database Based on PDB-Select at EMBL-Heidelberg FTP
- RDP - Ribosomal Database Project at U. Illinois W3
- ReBase - Restriction Enzyme Database and ReBase-Search at New England Biolabs, ReBase at EMBL-Heidelberg and ReBase at Johns Hopkins W3
- REPRO - Recognition of Protein Sequence Repeats at EMBL-Heidelberg W3
- RNA Secondary Structures - Information on Group I Introns and rRNA at U. Colorado-Boulder W3
- rRNA - Databases of Ribosomal Subunit RNA Sequences at U. Antwerp, Belgium W3
- RSVP - Rapid Sequence Visualization in Postscript for Analysis of DNA Sequences at CBIL-U. Pennsylvania W3
- SAPS - Statistical Analysis of Protein Sequences at ISREC, Switzerland W3
- SBASE - Library of Protein Domains and SBASE-Search at ICGEB-Trieste, Italy W3
- SCANPS - Scan Protein Sequences at U. Oxford, UK W3
- SCOP - Structural Classification of Proteins at Cambridge, UK and SCOP at U. South Florida W3
- Sequence Annotation - Annotations on NCBI Sequences at Baylor College of Medicine W3
- Sequence Translation - Translate Gene Sequences at U. Minnesota W3
- Sleuth - Amino Acid Conformation and Solvent Accessibility of PDB Files at Washington U. FTP
- SOPM - Self Optimized Prediction Method for Prediction of Protein Secondary Structure at IBCP-CNRS, France W3
- SRSWWW - Network Browser for Databanks in Molecular Biology (w/ diagram links) at EMBL-Heidelberg W3
- SRSWWW-Directory - Directory of SRSWWW Network Browsers for Biological Databanks and SRSWWW-Global Status at EMBnet-Basel W3
- SSEARCH - Universal Sequence Comparison Using the Smith-Waterman Algorithm at EERIE-Nimes, France W3
- SSPRED - Predict the Secondary Structure of Proteins at EMBL-Heidelberg, Germany W3
- STRIDE - Find Secondary Structural Elements in PDB Proteins Structures at EMBL-Heidelberg W3
- 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 W3
- SURVOL - Analysis of Protein Atomic Volumes at UCMB, Belgium W3
- Swiss-2DPage - Two-dimensional Polyacrylamide Gel Electrophoresis Database at ExPASy, Switzerland W3
- SWISSDOM - SwissProt Entries in a ProDom Map at EBI, UK W3
- Swiss-Model - Automated Protein Modelling at ExPASy, Switzerland W3
- SWISSNEW - New SwissProt Sequences at EBI, UK W3
- SwissProt - Protein Sequence Database (+ Weekly Updates) at ExPASy, Switzerland W3
- Swiss-Shop - Automated SwissProt and Prosite Information Queries at ExPASy, Switzerland W3
- TBASE - Transgenic/Targeted Mutation Database at Johns Hopkins W3
- TFASTA - Match a Protein Sequence Against All Six Frames of GenBank Sequences at EERIE-Nimes, France W3
- TFD - Transcription Factor Database at NIH Gopher
- TFFACTOR and TFSITE - Transcription Factor Data at EMBL-Heidelberg W3
- Tm - Oligonucleotide Melting Point Determination at U. Minnesota W3
- TMAP - Identification of Transmembrane Segments on a Protein Sequence at EMBL-Heidelberg W3
- TMBASE - Transmembrane Protein Database at U. Lausanne, Switzerland FTP
- TMpred - Prediction of Transmembrane Regions and Orientation in Protein Sequencs at ISREC, Switzerland W3
- Translate - Translate a Nucleotide Sequence to a Protein at ExPASy, Switzerland and Translate at EBI, UK W3
- TreeGen - Tree Generation from Distance Data at ETH-Zürich, Switzerland W3
- TREMBL - Database of Translated Peptide Sequences of All CDS Features from EMBL Sequences at EMBL-Heidelberg W3
- VecBase - Cloning Vector Sequence Database.at CAOS/CAMM, The Netherlands W3
- Vector-DB - Cloning Vector Database at Queen's U.-Kensington, Canada W3 , VECTOR at BEN, Belgium W3 , Vector at Johns Hopkins and Vector-ig at IVR, Kyoto-U., Japan Gopher
- VisAlign - The Alignment Color Viewer to Color 2 Aligned Amino Acid Sequences by Hydrophobicity at EBI, UK W3
- VisProt - The Protein Colorer to Color Amino Acid Sequences by Hydrophobicity at EBI, UK W3
- WebLogo - Sequence Logo Generation at Cambridge U., UK W3
- ZPRED - MultPredict Secondary Structure of Multiply Aligned Protein Sequences at Ludwig Institute for Cancer Research, UK W3
Last Modified: 96/06/15
pedro@iastate.edu