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Links to Molecular Biology Research Tools


Here you will find links and guides to handling and visualization of your own projects.


3D-ALI - Database relating Proteins Structures and Sequences (see Documentation) at EMBL-Heidelberg

AA Composition - Protein Identification in SwissProt using Amino Acid Composition at ExPASy, Switzerland

AA Similarity - Compare the Amino Acid Composition of a SwissProt Entry with Other Entries at ExPASy, Switzerland

BLAST - Basic Local Alignment Research Tool at NCBI

BLITZ at EMBL-Heidelberg

CATH Protein structure classification at UCL-London,

Codon Usage - Codon usage analysis at

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

DOTUP - Dotplot comparison of a DNA sequence with itself at Institut Pasteur

EMNEW - Index of New EMBL Sequences at EBI, UK

ENZYME - The Enzyme Data Bank at ExPASy, Switzerland

EPD - Eucaryotic Promoter Database at EMSwiss Institute for Bioinformatics

EPO - European Patent Office free search engine at espacenet,

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

FlyBase - Genetic and Molecular Database for Drosophila at Harvard U.

GDB - Human Genome Data Base at John Hopkins

Gene Finder - Predict Gene Structure, Internal Exons and Splicing Sites in DNA The Baylor College of Medicine

HSSP - Database of Homology-Derived Structures of Proteins based on PDB and SwissProt at EMBL-Heidelberg

LIGAND - Ligand Chemical Database for Enzyme Reactions at GenomeNet, Japan

Metabolic Database - Metabolic Reactions and Pathways at CGSC-Yale U. and Metabolic Database !Recent! at INRA-Moulon, France

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

MPBD - Molecular Probe Data Base at Istituto Nazionale per la Ricerca sul Cancro

MOTIF - Search Patterns in Protein Sequences at GenomeNet,

PredictProtein - Predict Protein Secondary Structure

OMIM - Online Mendelian Inheritance in Man at NCBI

Protein Data Bank Structures at Web Structure Download

Swiss-Prot - Search SwissProt for a Peptide Sequence at Expasy

PHD - Predict Protein Secondary Structure at EMBL-Heidelberg w/ search from Iowa State

PHILIP-Bootstrapping Analysis !Recent! - Divergence Between Protein or Nucleotide Sequences at Institut Pasteur, France

Phospepsort !New! - Digest Phosphorylated Peptide Sequences at EERIE-Nimes, France

pI/Mw - Compute the Theoretical pI and Molecular Weight of a Protein Sequence at ExPASy, Switzerland

Pileup !Recent! - Align Protein or Nucleotide Sequences at EERIE-Nimes, France

PIR - Protein Identification Resource Database at John 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 !Recent! - Predict Protein Secondary Structure at EMBL-Heidelberg

PRF - Protein Research Foundation Sequence Database at GenomeNet, Japan

Primer Selection - Select Primers in a Gene Sequence at U. Minnesota

PRINTS !Recent! - Protein Motif Fingerprints Database (see Documentation) at EMBnet-Basel, Switzerland

ProDom - A Protein Domain Database and ProDom-Search at Sanger Centre, UK, ProDom at EMBL-Heidelberg and ProDom-Info at Iowa State

ProLink - Integrated Database of Protein Structure, Sequence Homology, and Functional Pattern Information at BMERC (Gopher)

PROPSEARCH - Protein Sequence Search for Structural Homology Based on Aminoacid Properties at EMBL-Heidelberg

PROSITE - Protein Sites and Patterns Database at ExPASy, Switzerland and PROSITE-Search !Recent! at EMBL-Heidelberg

Protein-Extras at EMBL-Heidelberg (FTP)

Protein Families - Links to Information on Different Protein Families at Iowa State

Protein Motions !New! - DataBase of Protein Movements at Stanford U.

PSORT !Recent! - Predict Protein Sorting Signals Coded in Amino Acid Sequences at GenomeNet, Japan

PSSP !New! - Protein Secondary Structure Prediction at PUU - Protein Domains Database Based on PDB-Select at EMBL-Heidelberg (FTP)

RDP !New! - Ribosomal Database Project at U. Illinois

ReBase !New! - Restriction Enzyme Database at New England Biolabs, ReBase at EMBL-Heidelberg and ReBase at John Hopkins

RNA Secondary Structures - Information on Group I Introns and rRNA at U. Colorado-Boulder

Robert Kendall Photography - Land scape, Long exposure, and the beauty of nature at

rRNA !New! - Databases of Ribosomal Subunit RNA Sequences at U. Antwerp, Belgium

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. (FTP)

SOPM !New! - 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 !Recent! - Directory of SRSWWW Network Browsers for Biological Databanks and SRSWWW-Global Status !Recent! at EMBnet-Basel

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

SSPRED !New! - Predict the Secondary Structure of Proteins at EMBL-Heidelberg, Germany

SURVOL !New! - 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 !Recent! - Transgenic/Targeted Mutation Database at John Hopkins

TFASTA !Recent! - Match a Protein Sequence Against All Six Frames of GenBank Sequences at EERIE-Nimes, France

TFD - Transcription Factor Database at NIH (Gopher)

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 (FTP)

Translate !Recent! - Translate a Nucleotide Sequence into Amino Acid Sequence at EERIE-Nimes, France

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 !Recent! - Cloning Vector Sequence CAOS/CAMM, The Netherlands

VECTOR !Recent! - Cloning Vector Database at BEN, Belgium , Vector at John Hopkins and Vector-ig at IVR, Kyoto-U., Japan (Gopher)

WebLogo - Sequence Logo Generation at Cambridge U., UK

Macro Photography at - Macrophotography guide by Andrew Blyth at,

Wild animal photos - Exquisit photos of wild animals from around the world at,

Originally compiled by Pedro M. Coutinho at Iowa State University.

Data handling processing and evaluation

Data visualization

Graphical presentation

Photo Reference Library

Links to molecular biology research tools