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update by Class of Bioinformatics in Faculty of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Taiwan. date: 20041016.


Part 1: Molecular Biology Search and Analysis

*2* AA CompIdent- Protein Identification in SwissProt using Amino Acid Composition at ExPASy, Switzerland 
*2* AA CompSim - Compare the Amino Acid Composition of a SwissProt Entry with Other Entries at ExPASy, Switzerland 
*2* AbCheck- Test an Antibody Sequence Against the Kabat Database at U. College-London, UK
         *2* AllAll - Relationships in a Set of Related Peptides at ETH-Zürich, Switzerland
*2*ASC - Analytic Surface Calculation of PDB Protein Structures at EMBL-Heidelberg
          *2*BioBase - DNA Sequence Analysis Packages & Databases.
*2* Biologist's Search Palette - Collection of Search Engines for Biological Databases at Oxford U.
         *2* BioOpera- Process Support System for Molecular Sequence Analysis. A joint project between the 
               Information and Communication Systems and the CBRG.
*2* BLAST - Basic Local Alignment Research Tool at NCBI
*2* BLITZ (see Documentation)at EBI, UK 
*2* BLOCKS - Database of Highly Conserved Regions in Proteins at EMBL-Heidelberg
*2* BioMagResBank - A Database of NMR-Derived Protein Structures at BIMAS-NIH 
         *2* Codon Table- Japan [java].
         *2* Darwin-Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences at Computational 
               Biochemistry Research Group (CBRG).
*2* dbEST - Database of Expressed Sequence Tags at NCBI
*2* DBGET - Integrated Database Retrieval System (w/ diagram links) at GenomeNet, Japan
   *2* EBI -European Bioinformatics Institute
*2* EMBL - Nucleotide Sequence Database
*2* EMP Pathways - Enzyme and Metabolic Pathway (EMP) Database & its usage instruction.
*2* ENTREZ - Protein and Nucleotide Database (see Documentation) at NCBI
*2* ENZYME - The Enzyme Data Bank at ExPASy, Switzerland
*2* Enzyme Structures Database- Structures of Enzymes Deposited in the PDB at UCL-London, UK
*2* EPD - Eucaryotic Promoter Database at SRS-EMBL
*2* FASTA - Compare a Nucleic Acid Sequence to Nucleotide Sequence Databases (w/ updates) at EBI, UK
*2* FlyBase - Genetic and Molecular Database for Drosophila.
*2* GDB - Human Genome Data Base at Johns Hopkins
*2* GenBank Database (+Updates) at NCBI
*2* Gene Finder - find splice sites and protein coding exons, construct gene model and recognize the promotor and poly-A region.
*2* Grail - Analysis of the Protein Coding Potential of a DNA Sequence at ORNL
*2* GSDB - Genome Sequence Database at NCGR
*2* TagIdent tool (formerly GuessProt) at ExPASy.
*2* HOVERGEN - Database of Homologous Vertebrate Genes at CAOS/CAMM, The Netherlands 
*2* HPT - Protein Sequence Pattern Recognition in the PIR Database and HPT-Homology at MIPS, Germany
*2* HSSP - Database of Homology-Derived Structures of Proteins based on PDB and SwissProt at EMBL-Heidelberg 
*2* Kabat - Database of Proteins of Immunological Interest at Johns Hopkins 
*2* Kinemage-Index - "Kinetical Images" by Protein Type at Protein Science
*2* Klotho - Biochemical Compounds Declarative Database at Washington U.
*2* LALIGN - Calculates the N-Best Local Alignments Between Two Sequences at EERIE-Nimes, France
*2* LFASTA - Local Similarity Searches Between Two Sequences Showing Local Alignments at EERIE-Nimes, France 
*2* LIGAND - Ligand Chemical Database for Enzyme Reactions at GenomeNet, Japan 
*2* LiMB - Listing of Molecular Biology Databases at EMBL-Heidelberg 
*2* MassSearch- Search SwissProt or EMBL Databases by Protein Mass After Digestion at ETH-Zürich, Switzerland
             *2* MCS-Computational Biology at Argonne National Laboratory 
*2* Metabolic Database - Metabolic Reactions and Pathways at CGSC-Yale U.
*2* MGD - Mouse Genome Database at Jackson Laboratory 
*2* MHCPEP - Database of Major Histocompatibility Complex (MHC) Binding Peptides at WEHI-Melbourne, Australia 
          *2* MIPS- Munich information center for protein sequences.
*2* MIPS-Search - Automated Sequence Information Queries at MIPS, Germany 
*2* Molecules R US - Interactive Text and Images of PDB Files at NIH 
*2* MOOSE - Macromolecular Object Oriented Search Engine to Extract PDB Contained Information at Columbia U. 
*2* MSA - Multiple Sequence Alignment at Washington U. 
*2* MOTIF - Search Patterns in Protein Sequences at GenomeNet, Japan Motif at GenomeNet, Japan w/ search from Iowa State 
*2* Multiple Sequence Alignments - CLUSTAL-W, MAP, and PIMA alignments at Baylor College of Medicine
*2* NDB - The Nucleic Acid Database Project Rutgers, The State University of New Jersey
*2* nnPredict- Predict Protein Secondary Structure at UCSF and nnPredict at w/ search from Iowa State 
*2* NRL_3D - Sequence/Structure Database derived from PDB at Johns Hopkins and NRL_3D at EMBL-Heidelberg
*2* NRSub - A Non-Redundant DNA Sequence Database for Bacillus subtilis at National Institute of Genetics, Japan 
*2* NuclPepSearch - Search SwissProt for a Nucletide Sequence at ETH-Zürich, Switzerland 
*2* NYC-MASS - Protein Mass Spectrometry Database at Rockefeller U. 
*2* OBSTRUCT - Correlate Sequence Subsets of PDB Protein Structures at EMBL-Heidelberg 
*2* OMIM - Online Mendelian Inheritance in Man at Johns Hopkins 
*2* Organelle Genome  - A Sequence Database at U. Montreal 
*2* Organisms and Strains - Links to Databases Specific to Organism and Cell Collections at Biotech-Indiana 
*2* OWL - Non-Redundant Protein Sequence Database (Updated Daily) at UCL-London, UK 
*2* PatScan - Look for Pattern Matches in DNA or Protein Sequences at Argonne National Laboratory 
*2* PatternFind = Patternsearch - Search the SwissProt and Genpept Protein Sequence Databases with a PROSITE-formatted Pattern at ISREC, Switzerland 
*2* PDB- The Protein Data Bank is now maintained by the Research Collaboratory for Structural Bioinformatics (RCSB).
*2* PDB At A Glance - Hierarchic Access to PDB Files at NIH 
*2* PDBFINDER - A Database Containing PDB, DSSP and HSSP Information (see Documentation) at EMBL-Heidelberg 
*2* PDBSTR - Re-organized Protein Data Bank at GenomeNet, Japan 
*2* PepPepSearch - Search SwissProt for a Peptide Sequence at ETH-Zürich, Switzerland 
*2* Plant EST Analysis - Similarity Analysis of Different Plant cDNA/EST Sequences at U. Minnesota 
*2* PHD - Predict Protein Secondary Structure at EMBL-Heidelberg w/ search from Iowa State 
*2* PHILIP-Bootstrapping Analysis - Divergence Between Protein or Nucleotide Sequences at Institut Pasteur, France 
*2* Phospepsort - Digest Phosphorylated Peptide Sequences at EERIE-Nimes, France 
*2* pI/Mw - Compute the Theoretical pI and Molecular Weight of a Protein Sequence at ExPASy, Switzerland 
*2* PIR - Protein Identification Resource Database at Johns Hopkins 
*2* PIRALN - Database of Sequence Alignments based on PIR at EMBL-Heidelberg 
*2* PMD - Protein Mutant Database at GenomeNet, Japan 
*2* PMOTIF - Search Protein Motifs in Gene Sequence at U. Minnesota 
*2* Poland - Calculate the Thermal Denaturation Profile of Double Stranded RNA or DNA at Uni-Düsseldorf, Germany 
*2* PredictProtein - Predict Protein Secondary Structure at EMBL-Heidelberg 
*2* PRF - Protein Research Foundation Sequence Database at GenomeNet, Japan 
*2* 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.
*2* Primer at U. Minnesota
*2* PRINTS - Protein Motif Fingerprints Database (see Documentation) and PRINTS-ALIGN at UCL-London, UK
*2* ProDom - A Protein Domain Database is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases
*2* ProfileScan  - Search a Sequence Against a Library of Profiles at ISREC, Switzerland 
*2* ProLink - Integrated Database of Protein Structure, Sequence Homology, and Functional Pattern Information at BMERC 
*2* PROPSEARCH - Protein Sequence Search for Structural Homology Based on Aminoacid Properties at EMBL-Heidelberg 
*2* PROSITE - Protein Sites and Patterns Database at ExPASy, Switzerland, PrositeScan at ISREC, Switzerland and PROSITE-Search at EMBL-Heidelberg 
*2* Protein-Extras at EMBL-Heidelberg 
*2* Protein Families - Links to Information on Different Protein Families at Iowa State 
*2* Prot-ID - Identify a Protein from Masses of Enzymatic Digestion Peptide Fragments at Rockefeller U. 
*2* Protein Motions  - DataBase of Protein Movements at Stanford U. 
*2* PSA - Protein Sequence Analysis for Sequences of Unknown Structure at BMERC/MBCRR 
*2* PSORT - Predict Protein Sorting Signals Coded in Amino Acid Sequences at GenomeNet, Japan 
*2* PSSP - Protein Secondary Structure Prediction at
*2* PUMA2-Evolutionary Analysis of Metabolism - Phylogeny of Unicellular Organims with Metabolism and Alignments from MCS-Computational Biology at Argonne National Laboratory 
*2* PUU - Protein Domains Database Based on PDB-Select at EMBL-Heidelberg 
*2* RDP - Ribosomal Database Project at U. Illinois 
*2* ReBase - Restriction Enzyme Database and ReBase-Search at New England Biolabs, ReBase at EMBL-Heidelberg and ReBase at Johns Hopkins 
*2* RNA Secondary Structures - Information on Group I Introns and rRNA at U. Colorado-Boulder 
*2* rRNA - Databases of Ribosomal Subunit RNA Sequences at U. Antwerp, Belgium 
*2* SAPS - Statistical Analysis of Protein Sequences at EMBL-EBI
*2* SBASE - Library of Protein Domains and SBASE-Search  at ICGEB-Trieste, Italy 
*2* SCANPS - Scan Protein Sequences at U. Oxford, UK 
*2* SCOP - Structural Classification of Proteins at Cambridge, UK and SCOP at U. South Florida 
*2* Sequence Annotation - Annotations on NCBI Sequences.
*2* Sequence Translation - Translate Gene Sequences at U. Minnesota 
*2* Sleuth - Amino Acid Conformation and Solvent Accessibility (ftp) at Washington U. 
*2* SOPM - Self Optimized Prediction Method for Prediction of Protein Secondary Structure at IBCP-CNRS, France 
*2* SRSWWW - Network Browser for Databanks in Molecular Biology (w/ diagram links) at EMBL-Heidelberg 
*2* SRSWWW-Directory - Directory of SRSWWW Network Browsers for Biological Databanks.
*2* SSEARCH - Universal Sequence Comparison Using the Smith-Waterman Algorithm at EERIE-Nimes, France 
*2* STRIDE - Find Secondary Structural Elements in PDB Proteins Structures at EMBL-Heidelberg 
*2* 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 
*2* SURVOL - Analysis of Protein Atomic Volumes at UCMB, Belgium 
*2* Swiss-2DPage - Two-dimensional Polyacrylamide Gel Electrophoresis Database at ExPASy, Switzerland 
*2* SWISSDOM - SwissProt Entries in a ProDom Map at EBI, UK 
*2* Swiss-Model  - Automated Protein Modelling at ExPASy, Switzerland 
*2* SWISSNEW - New SwissProt Sequences at EBI, UK 
*2* SwissProt - Protein Sequence Database (+ Weekly Updates) at ExPASy, Switzerland 
*2* Swiss-Shop  - Automated SwissProt and Prosite Information Queries at ExPASy, Switzerland 
*2* TBASE - Transgenic/Targeted Mutation Database at Johns Hopkins 
*2* TFASTA - Match a Protein Sequence Against All Six Frames of GenBank Sequences at EERIE-Nimes, France 
*2* TFD - Transcription Factor Database at NIH 
*2* TFFACTOR and TFSITE - Transcription Factor Data at EMBL-Heidelberg 
*2* Tm - Oligonucleotide Melting Point Determination at U. Minnesota 
*2* TMAP - Identification of Transmembrane Segments on a Protein Sequence at EMBL-Heidelberg 
*2* TMBASE - Transmembrane Protein Database at U. Lausanne, Switzerland 
*2* TMpred - Prediction of Transmembrane Regions and Orientation in Protein Sequencs at ISREC, Switzerland 
*2* Translate - Translate a Nucleotide Sequence to a Protein at ExPASy, Switzerland 
*2* TreeGen - Tree Generation from Distance Data at ETH-Zürich, Switzerland 
*2* VecScreen - is a system for quickly identifying segments of a nucleic acid sequence that may be of vector origin.
        *2*  cVECTOR-The cloning vector collection, Japan. 
*2* WebLogo - Sequence Logo Generation at Cambridge U., UK 
 

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Last Modified: 95/06/15


pedro@iastate.edu