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Special Friend of BioPlanet:
Bio-Web - Resources for Molecular and Cell Biologist
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The main list is maintained by ICP and has been mirrored with their permission. Compiled by Mark Van Ranst(KUL). Updated and adapted for use on the internet by Fred Opperdoes(UCL). Please report broken links to FredOpperdoes |
Index of links
GENERAL DATABASE INFO
- Database Statistics (courtesy of DDBJ)
- Human Genome Sequencing
- GENBANK (NCBI)
- GENBANK SITEMAP
- EMBL (EBI)
- PDB Protein 3D database
- Nucleotide sequences at EBI
- Nucleotide sequences at GenBank
- MAGPIE - Multipurpose Automated Genome Project Investigation Environment
- DDBJ (DNA Data Bank of Japan)
- MBGD Microbial Genome Database
- HOX Pro DataBase (in Russia)
- HOX Pro DataBase (Mirror in the US)
- Expasy Home of SwissProt Protein database
- SWISS-PROT (ExPasy)
- The Sanger Centre
- Genome Monitoring Table (daily update EBI)
- MAGPIE
- NIH News Release 06/26/2000
- Enzyme Nomenclature
- TIGR Microbial Database
- Pfam Protein domain database at Sanger Centre
- The TIGR Trypanosoma brucei Database
- Trypanosome GeneDB at Sanger
- BMERC Completed Genomes collected resources
- DNA Sequence Collaborator's Page
- Genome Sequence Database GSDB (NCGR)
- PEDANT complete genome analysis
- C. elegans Database
- The Protein Research Foundation
- Population studies with PopSet with aligned DNA seqiences
- Extinct organisms in GenBank
- DBGET Database Document: GenBank
SEQUENCE SUBMISSION
- GENBANK BankIt
- GENBANK Sequin
- EMBL Webin
- DDBJ Sakura
Vector screeningSEQUENCE RETRIEVAL
DNA
- ENTREZ-Nucleotide query (NCBI)
- SRS at EMBL-EBI, Hinxton (UK)
- DNA Search (GenomeNet, Japan)
- GENBANK at NCBI
- Direct retrieval from EMBL via accession code
PROTEIN
- ENTREZ-Protein query (NCBI)
- SRS at EMBL-EBI, Hinxton (UK)
- Protein Search (GenomeNet, Japan)
- SWISS-PROT and TrEMBL (Switzerland)
- RCSB Protein Data Bank (US)
- RCSB PDB Mirror Sites
- PIR-Web - The Protein Identification Resource (NONACTIVE)
- GENBANK using ENTREZ
- Protein Search (GenomeNet, Japan)
- Direct retrieval from EMBL via accession code
ALERT SERVERS
- EMBL Sequence Alerting System
- SWISSPROT alert server
- BEN sequence awareness service (registered users only)
- BEN sequence similarity awareness service (registered users only)
GENOMICS
GENERAL GENOMICS
- Entrez-Genome (NCBI)
- Genome Monitoring Table (daily update EBI)
- NCGR National Center for Genome Resources
- Genome Channel (Oak Ridge, US) *
- Organism-specific Databases
- GOLD: Genomes OnLine Database Homepage
- PEDANT front page
- NIH News Release 06/26/2000
- The Human Genome, by All of the Top Cartoonists
HUMAN GENOME PROJECT
NIH/NCBI HUMAN GENOME RESOURCES
- The Human Genome
- Entrez Genome view: MAPVIEWER
- LocusLink Introduction
- Human Genome Sequencing
- National Human Genome Research Institute (NHGRI)
- dbSNP Home Page
- NCBI Contig Build and Annotation Process
ENSEMBL (EBI/Sanger Institute)
- Ensembl Genome Server (not active)
HUGO (Human Genome Organisation)
OMIM (Online Mendelian Inheritance in Man)
GENECARDS
- GeneCards (Weizmann Institute, Israel)
- GeneCards mirror (Finland)
- GeneCards mirror (Germany)
- GeneCards mirror (Canada)
- GeneCards mirror (Japan)
DDBJ/CIB HUMAN GENOMICS STUDIO
HGSC Human Genome Sequencing Center (Baylor College of Medicine)
ONL Oak Ridge National Laboratory
ETHICAL, LEGAL, SOCIAL ASPECTS
OTHER GENOME PROJECTS
EUKARYOTIC GENOME PROJECTS
- Mouse Genome Resources Page
- Rat Genome Resources Page
- Zebrafish Genome Resources Page
- Drosophila melanogaster @ NCBI
- Malaria Genetics & Genomics
- C. elegans project
- Arabidopsis thaliana
PARASITE GENOME PROJECTS
- Trypanosoma brucei Genome Project
- Leishmania Genome Network
- Trypanosoma brucei home page (at Sanger)
- Trypanosoma brucei Genome Network home page
- Trypanosoma brucei GSS sequences for downloading
- The TIGR Trypanosoma brucei Database
- Trypanosome GeneDB at Sanger
- Trypanosoma cruzi Blast search at TIGR
- Leishmania major home page (at Sanger)
- Leishmania Genome Network home page
- Leishmania major chromosome 15
- Leishmania major chromosome 26
- Leishmania major chromosme 28
- Leishmania Genome Network, Seattle, USA
- Parasite-genome database at EBI
- Parasite genome Blast server at EBI
- Parasite genomes databasesWHO Leishmania Genome Network Web site
- Malaria (Plasmodium falciparum genome map)
- Plasmo DB (Plasmodium Genome database)
MICROBIAL GENOME PROJECTS
- PEDANT complete genomes
- Entrez: microbial genomes taxonomy tree
- TIGR Microbial Database
- DDBJ Genome Information Broker
VIRAL GENOME PROJECTS
COMPARATIVE GENOMICS
COMPLETE GENOMES AND GENOME PROJECTS
- GOLD Genome On line Database
- Proteome analysis at EBI
- All Available Complete Genomes
- GeneQuiz (Genome annotations)
- LocusLink (Human, Mouse and Rat Loci)
- Entrez Genomes Views (Human Chromosomes)
- Mitochondrial Genomes Database
- GOBASE - The Organelle Genome Database
- Saccharomyces Genome Database
- Mycoplasma genitalium database (not available)
- Haemophilus influenzae database (not available)
- Methanococcus jannaschii database (not available)
- E. coli genome center
- Heliobacter pylori database (not available)
- E. coli database collection (not available)
- Sanger Center C. elegans homepage (not available)
- Bacillus subtilis database
- Genome Sequencing Center, St. Louis
- Methanobacterium thermoautotrophicum abstract
- The Genome Database
- Sanger Center S. pombe homepage (not available)
- Human Genome Project Infor
- Mouse Genome Databasemation (not available)
- Arabidopsis thalianaProject
- Arabidopsis genome completed (Nature paper, 2000)
- Flybase(not available)
- Drosophila database
- TIGR Arabidopsis thaliana Database
- TIGR Archaeoglobus fulgidus Database(not available)
- TIGR Borrelia burgdorferi Database(not available)
- Pyrococcus furiosus news article
- Pyrobaculum aerophilum abstract(not available)
- Sulfolobus solfataricus P2 complete genome
- Borrelia burgdorferi news article
- Yersinia Pestis complete genome
- HOBACGEN (the Homologous Bacterial Genes Database)
GENE PREDICTION
- EMBOSS at EBI
- Gene Finder at Sanger centre
- PredictGenes (Darwin) (Switzerland)
- SBDS sequence analysis
- Bipartite Nuclear Localisation Sequence Locator
- IUPAC-IUB Abbreviations and symbols for nucleic acids, polynucleotides and their constituents.
- GENSCAN at MIT (US) ***
- WebGeneMark
- GrailEXP at Oak Ridge (US)
- Genie at Berkeley (US)
- Gene Prediction Services
TRANSLATION
- EMBOSS at EBI
- ExPASy - Translate tool
- DNA Sequence Translation (ALCES)
- The Protein Machine (EBI)
- Nucleic Acid to Amino Acid Translation (London)
- Nucleic Acid to Amino Acid Translation (London - mirror)
- SeWeR is a DHTML interface for web based sequence analysis
- IUBMB Prokaryotic and eukaryotic translation factors.
ORF ANALYSIS
- EMBOSS at EBI
- ORF Finder (NCBI)
- ORF analysis (WebGene)
- FGENESH-2 Improving gene finding accuracy
- FGENESH HMM - Gene finding for mouse genes
TRANSCRIPTION FACTOR BINDING SITES
REPEATS
- EMBOSS at EBI
- Dot Plot Analysis THEORETICAL EXPLANATION
- Dot Plots (Colorado State University) (limit: 20.391bp x 20.391 bp)
- Dot Plot (to itself) (ALCES) (postscript/GIF output)
- Blast 2 Sequences (NCBI)
CODON USAGE
CONTIG ASSEMBLY
PATTERN SCAN
RESTRICTION ENZYME
RE ANALYSIS
- Webcutter 2.0 (USA)
- Webcutter 2.0 (USA)
- Webcutter 2.0 (Sweden)
- Restriction Enzyme Analysis (SUNY) (US)
- Restriction Maps (Colorado) (US)
- REMAP
- MBS - SeqCUTTER - On-line enzyme restriction analysis tool
- MULTI-CUT Restriction Endonuclease Buffer Data Base
RE LISTS
RE SUPPLIERS
OLIGO/PRIMER ANALYSIS
- WWW GeneFisher (Germany) ***
- PCR Aplification Assistant
- IDT OligoAnalyzer 2.0 (US) ***
- Oligonucleotide Calculator (USA) - simple
- GENSET OLIGOS - Oligo Calculation
- Tm Determination (ALCES) - simple
- pDRAW32 - freeware DNA cloning, sequence analysis and plasmid/DNA plotting software
- Oligonucleotide Calculator (USA) - simple
- WWW GeneFisher
- Primer3 at MIT (US)
- Primer3 (older version)
- Primer Selection (Text) (ALCES)
- NetPrimer (US)
- NCBI Blast short sequence
- Visual Cloning 2000 (Redasoft)
- PCR Box Titration Calculator v 0.93
- Alkami Biosystems: Primer Design Online
- Web Primer: DNA and Purpose Entry
- CODEHOP
- netprlaunch
- Tavi's PCR protocols
SEQUENCE-FORMAT CONVERSIONPAIRWISE SEQUENCE ALIGNMENT
- BCM: Pairwise Sequence Alignment
- Dot/matrix plots
- Dotmatrix program PPCMatrix
- LALIGN (france)
- Blast 2 Sequences (NCBI)
- SBDS: Pairwise Sequence Alignment (works only well for proteins)
- MBS - ALIGNER : CLUSTALW interface for multiple sequence alignement (did not work on netscape navigator)
MULTIPLE SEQUENCE ALIGNMENT
- BCM: Multiple Sequence Alignments
- IBC: Multiple sequence alignment (MSA)
- SAM: Sequence Alignment and Modeling System
- CLUSTALW at GenomeNet (Japan)
- ClustalW at EBI (UK)
- CLUSTALW at DDBJ (Japan)
- CLUSTALW at IBCP (WWW to EMAIL)
- GeneBee ClustalW 1.75
- CMBI CLUSTAL W
- MULTALIN at IBCP (WWW to EMAIL)
- MULTALIN + CLUSTAL at IBCP (WWW to EMAIL)
ALIGNMENT VISUALISATION/EDITING/FORMATTING
BLAST
- BLAST at NCBI (USA) - basic
- BLAST at NCBI (USA) - advanced
- BLAST against (un)finished Genomes at NCBI (USA)
- MEGABLAST at NCBI (large set of DNA query sequences)
- MEGABLAST at Harvard (large set of DNA query sequences)
- Search for short nearly exact matches of DNA sequences
- Search for short nearly exact matches of protein sequences
- PSI BLAST at NCBI (USA) - Position Specific Iterated BLAST
- BLAST 2 sequences
- BLAST at EBI (Hinxton, UK)
- BLASTall at EBI (Hinxton, UK)
- BLAST at GenomeNet (Japan)
- BLAST at BCM: DNA searches
- BLAST at BCM: Protein searches
- BLAST at PIR-International Protein Sequence Database
- BLAST search in PRODOM
- OWL BLAST Server
- GeneBee Basic BLAST 2.0
- Genebee Advanced BLAST 2.0
FASTA
SW (Smith-Waterman)
BASED ON AA COMPOSITION
DARWIN
RNA
- RNA folding (Zuker)
- RNA folding (Zuker, older version, allows variable temp)
- RNA folding (Zuker; mirror at Wayne State University)
- RNA folding (Zuker; mirror in Australia)
returns results by email only.PROTEIN
- AGADIR An algorithm to predict the helical content of peptides
- SSCP Secondary structural content prediction from amino acid composition
- Southampton - SBDS - GOR
- CPHmodels - Homology modelling
- PREDATOR request form
- Southampton - SBDS - GOR
- IBCP secondary structure (France)
- Protein Explorer FrontDoor (Univ Mass)
- Protein Explorer FrontDoor (San Diego, faster)
- PredictProtein
- 3D-PSSM Protein Fold Recognition (Threading) Server (UK)
- Description of SSThread WWW service
- GENO3D : AUTOMATIC MODELING OF PROTEINS THREE-DIMENSIONAL STRUCTURE
- BCM: Secondary Structure Prediction
- PREDATOR request form
- EMBL Dali: email server for 3-D protein structure database searches
- BCM PSSP
- CE Home Page - Combinatorial Extension
- SSCP: protein -> AA composition -> SS (EMBL) (WWW to EMAIL)
- SSCP: AA composition -> SS (EMBL) (WWW to EMAIL)
- TMAP (EMBL) (WWW to EMAIL)
- PDB to Animated Gif
- Download RASMOL
- Sander's 3-D Modelling homepage
- List of free molecular visualization programs
- Structural Biology Software Database
- MDL Information Systems, Inc | Chime Plug-in
Software Programmes
- Joe Felsenstein's Phylogeny programs website
- Phylogenetic Analysis Computer Programs
- Phylogeny software (Glasgow University)
- TreeTop - Phylogenetic Tree prediction
- CMBI CLUSTAL W
- Puzzle: Tree reconstruction for sequences by quartet puzzling and maximum likelihood (Strimmer, von Haeseler)
- MacClade Home Page
- PAUP
- Morkov Chain Monte Carlo - phylogeteic analysis (USA)
- Morkov Chain Monte Carlo - phylogeteic analysis (UK)
- Morkov Chain Monte Carlo - Molecular clock
- TREECON download page (demo version)
- Phylogeny server at Pasteur
- SOAP Stability of aligned positions
- TreeEdit
- FORCON download page (sequence format interconversion for the PC only)
- Mesquite
Databases
- TreeBase at Harvard
- Aligned DNA and Protein sequences at EBI
- Molecular Evolution & Organelle Genomics
Info and tutorials
Protein Database Brookhaven PDB/RSCB Protein Data Bank
- 3DB Browser (Brookhaven, main site)
- 3DB Browser (EBI, mirror)
- 3DB Browser (UK, mirror)
- 3DB Browser (Germany, mirror)
- 3DB Browser (Poland, mirror)
- 3DB Browser (France, mirror)
- PDB WWW Home Page
- PDB At A Glance
- PDB Retriever at DDBJ
- RCSB Protein Data Bank at SDSC (main)
- RCSB Protein Data Bank at Rutgers (mirror)
- RCSB Protein Data Bank at NIST (mirror)
- RCSB Protein Data Bank (all mirror sites)
CHIME 3D
SEQUENCE ANALYSIS TOOLS
- Direct access to seuence analysis tools at the Pasteur Institute
- SeWeR is a DHTML interface for web based sequence analysis
CMS-SDSC MOLECULAR BIOLOGY RESOURCE
- The CMS-SDSC Molecular Biology Resource - France
- The CMS-SDSC Molecular Biology Resource - San Diego (US)
- The CMS-SDSC Molecular Biology Resource - Italy
- The CMS-SDSC Molecular Biology Resource - United Kingdom
PEDRO'S BIOMOLECULAR RESEARCH TOOLS
TUTORIALS AND COURSES ON THE WEB
SOFTWARE FOR SEQUENCE ANALYSIS
PHYLOGENY
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Last updated: 1 Nov, 2002
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