Part 1: Molecular Biology Search and Analysis

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 

AbCheck- Test an Antibody Sequence Against the Kabat Database at U. College-London, UK

         AllAll - Relationships in a Set of Related Peptides at ETH-Zürich, Switzerland

ASC - Analytic Surface Calculation of PDB Protein Structures at EMBL-Heidelberg

          BioBase - DNA Sequence Analysis Packages & Databases.

Biologist's Search Palette - Collection of Search Engines for Biological Databases at Oxford U.

         BioOpera- Process Support System for Molecular Sequence Analysis. A joint project between the 

               Information and Communication Systems and the CBRG.

BLAST - Basic Local Alignment Research Tool at NCBI

BLITZ (see Documentation)at EBI, UK 

BLOCKS - Database of Highly Conserved Regions in Proteins at EMBL-Heidelberg

BioMagResBank - A Database of NMR-Derived Protein Structures at BIMAS-NIH 

         Codon Table- Japan [java].

         Darwin-Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences at Computational 

               Biochemistry Research Group (CBRG).

dbEST - Database of Expressed Sequence Tags at NCBI

DBGET - Integrated Database Retrieval System (w/ diagram links) at GenomeNet, Japan

   EBI -European Bioinformatics Institute

EMBL - Nucleotide Sequence Database

EMP Pathways - Enzyme and Metabolic Pathway (EMP) Database & its usage instruction.

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 SRS-EMBL

FASTA - Compare a Nucleic Acid Sequence to Nucleotide Sequence Databases (w/ updates) at EBI, UK

FlyBase - Genetic and Molecular Database for Drosophila.

GDB - Human Genome Data Base at Johns Hopkins

GenBank Database (+Updates) at NCBI

Gene Finder - find splice sites and protein coding exons, construct gene model and recognize the promotor and poly-A region.

Grail - Analysis of the Protein Coding Potential of a DNA Sequence at ORNL

GSDB - Genome Sequence Database at NCGR

TagIdent tool (formerly GuessProt) at ExPASy.

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 EMBL-Heidelberg 

MassSearch- Search SwissProt or EMBL Databases by Protein Mass After Digestion at ETH-Zürich, Switzerland

             MCS-Computational Biology at Argonne National Laboratory 

Metabolic Database - Metabolic Reactions and Pathways at CGSC-Yale U.

MGD - Mouse Genome Database at Jackson Laboratory 

MHCPEP - Database of Major Histocompatibility Complex (MHC) Binding Peptides at WEHI-Melbourne, Australia 

          MIPS- Munich information center for protein sequences.

MIPS-Search - Automated Sequence Information Queries at MIPS, Germany 

Molecules R US - Interactive Text and Images of PDB Files at NIH 

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 - The Nucleic Acid Database Project Rutgers, The State University of New Jersey

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 UCL-London, UK 

PatScan - Look for Pattern Matches in DNA or Protein Sequences at Argonne National Laboratory 

PatternFind = Patternsearch - Search the SwissProt and Genpept Protein Sequence Databases with a PROSITE-formatted Pattern at ISREC, Switzerland 

PDB- The Protein Data Bank is now maintained by the Research Collaboratory for Structural Bioinformatics (RCSB).

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 

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 

QPPD -The Quantitative PCR Primer Database provides information about primers and probes that can be used to quantitate human and mouse mRNA by RT–PCR.

Primer at U. Minnesota

PRINTS - Protein Motif Fingerprints Database (see Documentation) and PRINTS-ALIGN at UCL-London, UK

ProDom - A Protein Domain Database is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases

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

PUMA2-Evolutionary Analysis of Metabolism - 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 

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 

SAPS - Statistical Analysis of Protein Sequences at EMBL-EBI. 

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.

Sequence Translation - Translate Gene Sequences at U. Minnesota 

Sleuth - Amino Acid Conformation and Solvent Accessibility (ftp) 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.

SSEARCH - Universal Sequence Comparison Using the Smith-Waterman Algorithm at EERIE-Nimes, France 

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 

VecScreen - is a system for quickly identifying segments of a nucleic acid sequence that may be of vector origin.

          cVECTOR-The cloning vector collection, Japan. 

WebLogo - Sequence Logo Generation at Cambridge U., UK 

 

I welcome any comments or suggestions of changes to this Page!

Last Modified: 95/06/15