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
