Pedro's BioMolecular Research Tools - Part 1

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

This is just a (slightly modified) mirror of Pedro's Research Tools PART 1, July 16, 1996 update. For the rest, go to original Pedro's site .

Updates: November 12, 1997 (changed ExPASy location); ...