
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![[L]](./images/smiley.gif)
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![[L]](./images/smiley.gif)
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![[L]](./images/smiley.gif)
- 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