Pedro's Search and Analysis Tools

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Contributed URL's

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
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
3Dee Database of structural domain definitions in proteins and their classification (Submitted by Asim Siddiqui as@bioch.ox.ac.uk)
Match-Box Multiple sequence alignment server at the University of Namur, Belgium. (Submitted by Guy Baudoux Guy.Baudoux@fundp.ac.be)

Bio-wURLd is a searchable, user-maintained collection of URL's related to bioinformatics, biochemistry, and molecular biology.