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Bioinformatics links |
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Please report broken links to Fred Opperdoes
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Bioinformatics links |
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Recent additions to
the list Number of
visitors since 24 Sept 2000
EMBOSS
at EBI a suiteof
DNA and protein analysis programs
FastCounter
by bCentral
Techniques
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
- NCBI's Cn3D
- 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: 27 Sep, 2003
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