BioInformatics Links

DNA/PROTEIN DATABASES

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 screening

• VecScreen (NCBI)
• Vector Scanning (EBI)
• Vector Screening System (DDBJ)

SEQUENCE 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)

• HUGO homepage
• HUGO human chromosomes page
• HUGO Gene Nomenclature Committee (HGNC)

OMIM (Online Mendelian Inheritance in Man)

• OMIM - Online Mendelian Inheritance in Man

DDBJ/CIB HUMAN GENOMICS STUDIO

• DDBJ/CIB Human Genomics Studio

GENECARDS

• GeneCards (Weizmann Institute, Israel)
• GeneCards mirror (Finland)
• GeneCards mirror (Germany)
• GeneCards mirror (Canada)
• GeneCards mirror (Japan)

HGSC Human Genome Sequencing Center (Baylor College of Medicine)

• Welcome to Baylor HGSC

ONL Oak Ridge National Laboratory

• Human Genome Landmarks Poster
• Human Genome Project Information

ETHICAL, LEGAL, SOCIAL ASPECTS

• Clinical and patient aspects (HUGO)
• Ethical, Legal and Social Implications (ELSI; NHGRI at NIH)

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

MICROBIAL GENOME PROJECTS

• PEDANT complete genomes
• Entrez: microbial genomes taxonomy tree
• TIGR Microbial Database
• DDBJ Genome Information Broker

VIRAL GENOME PROJECTS

• Complete viral genomes (NCBI)
• Retroviruses

 

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)

COMPARATIVE GENOMICS

• PEDANT CrossGenome categories
• COG: Clusters of Orthologous Groups of proteins( NCBI)
• TaxPlot (NCBI)
• HOBACGEN Homologous Bacterial Genes Database

• WIT Home Page
• KEGG Kyoto Encyclopedia of Genes and Genomes
• ERGO (Integrated Genomics, Inc.)
• LION bioscience | Products and Services | genomeSCOUTô

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)

TAXONOMY

• NCBI Taxonomy Homepage
• Taxonomy Browser at NCBI
• The Tree of Life Home Page
• Introduction to Phylogeny

RIBOSOMAL RNA

• Ribosomal Database Project II (USA)
• The rRNA WWW Server (UIA Antwerp)

DNA SEQUENCE ANALYSIS

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

• TFSEARCH: Searching Transcription Factor Binding Sites
• MatInspector (Germany)
• Alibaba2 (Germany)

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

• Codon Usage Database
• Codon usage (ALCES)
• GCUA (Thomas Schoedl's Graphical Codon Usage Analyser)

CONTIG ASSEMBLY

• CAP sequence assembly at Infobiogen
• CAP Sequence Assembly at BCM Search Launcher

PATTERN SCAN

• PatScan

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

• REBASE at NEB

RE SUPPLIERS

• Restriction Endonuclease Suppliers (Multi-Cut site)

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
  

SIMPLE NUCLEOTIDE MANIPULATIONS

• Reverse/Inverse/Inverse complement (Colorado State University)
• BCM: Sequence Utilities (inverse, complement)
• MBS - SeqCLEANER - Clean up your sequences from databases marks

• The Sanger Centre : Java View ABI traces at Sanger

PROTEIN SEQUENCE ANALYSIS

• EMBOSS at EBI
• Match-Box server
• HOX Pro DataBase (in Russia)
• HOX Pro DataBase (Mirror in the US)
• PirAlin protein alignment database
• Entrez-Protein
• SWISS-PROT and TrEMBL
• PIR-Web - The Protein Identification Resource
• Protein Search (GenomeNet, Japan)
• PirAlin protein alignment database
• Enzyme Nomenclature
• Pfam Protein domain database at Sanger Centre
• Darwin, a Computational Biochemistry Research Tool
• Readseq - biosequence conversion tool
• SeWeR is a DHTML interface for web based sequence analysis

 

AMINO ACID/PROTEIN INFORMATION

• Genetic Code Viewer
• single letter amino acid codes
• amino acid structures
• BRENDA the enzyme database
• IUBMB enzyme nomenclature
• IUPAC-IUB: phosphorus-containing compounds of biochemical importance
• IUPAC-IUB : synthetic polypeptides - Polymerised amino acids.

HYDROPHOBICITY PLOT

• Hydropathicity Plots at Colorado (US)

REVERSE TRANSLATION

• Reverse Translate a Protein at Colorado (US)

MOTIFS / PATTERNS SEARCHING

• NPS@ : PATTINPROT search
• PROSITE at EBI (Hinxton, UK))
• PROSITE at ExPASy (Switzerland)
• PRATT at EBI (input alignment) ***
• FPAT Regular Expression Searching Protein Databases
• MIPS ATLAS
• PatScan (also imperfect matches)
• ISREC PatternFind (WWW to EMAIL)
• Motif Explorer
• N-Glycosylation Site Prediction Server
• CBS prediction servers
• BNL motif searching
• SignalP signal peptide identification
• Sigfind signal peptide identification
• MOTIFS in SwissProt at IBCP (France)(WWW to EMAIL)
• PRINTS
• BLOCKS
• PRODOM
• SBASE
• MOTIF at GenomeNet (Japan)
• Protein Motifs (ALCES)
• PROTCOMP Identification of sub-cellular localization of eukaryoric proteins

GENEQUIZ

• GQserve - Public GeneQuiz Server ***

PREDICTPROTEIN

• The PredictProtein server
• PPstatus: What is the PP backlog ?

DARWIN

• Darwin, a Computational Biochemistry Research Tool
• TreeGen: Tree generation from distance data
• AllAll: Related peptide sequences
• AllAllDB: Querying the all-against-all database of SwissProt
• NuclPepSearch: Searching SwissProt for a nucleotide sequence
• PepPepSearch: Searching SwissProt for a peptide sequence
• darwin: Run a Darwin program

STATISTICAL ANALYIS

• Statistical Analysis of Protein Sequences at EBI (Hinxton, UK)
• SAPS at ISREC (Switzerland)

DIGESTION PRODUCTS SEARCH

• MOWSE
• PROWL
• MassSearch: Searching SwissProt or EMBL by protein mass after digestion

PROTEIN SORTING / LOCALIZATION

• PSORT (Japan)
• PROTCOMP Identification of sub-cellular localization of eukaryoric proteins
• SignalP signal peptide identification

ISO-ELECTRIC POINT / MOLECULAR WEIGHT

• protein -> pI, MW and Composition
• protein -> pI and MW (EXPASY)

AMINO ACID COMPOSITION

• Protein -> AA composition (SBDS)
• Protein -> AA composition + analysis (SAPS at ISREC)
• AA composition -> protein search (EXPASY)
• AA composition -> protein search (EMBL)
• AA composition -> Sec. Str. (EMBL) (WWW to EMAIL)
• MBS - ProtCALC - protein parameters (pI, MW, aa composition, Extinction data)

ProtoMap - Main

CGG Protein sequence analysis

METABOLIC PATHWAYS

SEQUENCE ALIGNMENT

SEQUENCE-FORMAT CONVERSION

• Readseq - biosequence conversion tool
• Readseq - at Iubio Indiana USA

PAIRWISE 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

  • BoxShade Server (Switzerland) ***
  • ForCon homepage
  • CINEMA (Colour INteractive Editor for Multiple Alignments)

SEQUENCE HOMOLOGY SEARCHES

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

• FASTA at EBI (Hinxton, UK)
• FASTA at NPS (France)
• FASTA Email server at EBI
• Fasta 3.3

SW (Smith-Waterman)

• Smith-Waterman (EBI)

BASED ON AA COMPOSITION

• AA composition: protein search (ExPASY)
• AA composition: PropSearch (EMBL)

DARWIN

• AllAll: Related peptide sequences
• AllAllDB: Querying the all-against-all database of SwissProt
• NuclPepSearch: Searching SwissProt for a nucleotide sequence
• PepPepSearch: Searching SwissProt for a peptide sequence

• PROPSEARCH (EMBL) (WWW to EMAIL)
• EMBL Dali: email server for 3-D protein structure database searches

SECONDARY/TERTIARY STRUCTURE PREDICTION

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

PHYLOGENY

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

• Harvard Dept of MCB - More Biology Links
• Tree of Life Homepage
• Phylogenetic Analysis of Proteins (Fred Opperdoes)
• Introduction to Phylogeny

MEDLINE

• NCBI PubMed
• BioMedNet MEDLINE
• MEDLINE Alert service (at EMBL)
• BioMail, References from Medline to your e-mail account
• Biomail via Russia

3D PROTEIN IMAGES

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

• Chemscape Chime: download page
• Molecular Tutorials using Chemscape Chime from MDL Information Systems
• HIV-1 protease -- structure with indinavir

• ENZYME database
• BRENDA the enzyme database
• PROTEIN EXPLORER (3D PDB online viewer)
• Swissmodel
• PDB to MultiGif Page
• SWissPdbViewer Tutorial
• Swiss-PdbViewer: Superimposition
• Swiss-PdbViewer (download page)
• Pro3D download page
• Entrez structure query
• SCOP: Structural Classification of Proteins
• CATH (classification of protein structures)
• WebLab Viewer download page
• WebLab Viewer Operating Systems
• FSSP
• NRL_3D-Web
• Molecules-R-US
• The NIH Molecular Modeling Home Page
• ExPASy - SWISS-3DIMAGE
• Protein Science KINEMAGE database
• Image Library of Biological Macromolecules
• EMBL Dali: email server for 3-D protein structure database searches
• PDB to Animated Gif
• Sander's 3-D Modelling homepage
• PRF The Protein Research Foundation (Japan)
• NCBI's Cn3D

• BioCarta - Charting Pathways
• BRENDA the enzyme database
• SwissProt/TrEMBL
• Enzyme database
• Boehringer metabolic pathways
• KEGG metabolic encyclopedia
• KEGG metabolic encyclopedia2

• EMP - Enzymes and Metabolic Pathways Project
• aMAZE Protein function and biochemical pathways database
• Pedant
• WIT database
• COG (Clusters of orthologous Groups) database
• EcoCyc E.coli database
• Malaria parasite metabolic pathways
• List of metabolic pathway databases

GENERAL BIOINFORMATICS SITES

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

• Pedro (original site in US)
• Pedro (mirror in Germany)
• Pedro (mirror in Switzerland)
• Pedro (mirror in US)

• MolBiol.Net - Portal for Web-Based Molecular Biology Tools
• IUBMB Biochemical nomenclature site
• BioMail, References from Medline to your e-mail account
• Biomail via Russia
• ProMED Emerging Diseases Website
• Directory of sequence analysis tools at Pasteur, France
• Swiss-Quiz Molecular Biology Quiz
• SBDS sequence analysis
• NPS@: Welcome to Network Protein Sequence @nalysis at IBCP, FRANCE
• Klotho: Biochemical Compounds Declarative Database
• Practical Biocomputing
• IBC Internet services for molecular biology computing
• EMBL Dali: email server for 3-D protein structure database searches
• Workshop for DNA and Protein Seque
• BIOCIENCE vital links
• The Institute for Genome Research
• GenQuest - The Q server
• Welcome to G…N…THON Web server
• Internet for the Molecular Biologist
• Molecular Biology Jump Station
• Microbiology Jump Station
• GENOME WORKSTATION
• BIOCCELERATOR Home Page
• Freiburg search tools
• MIPS: Martinsried Institute for Protein Sequences
• European Molecular Biology Laboratory (EMBL)
• GenomeNet WWW server
• NIH Home Page
• ABIM Online analysis tools
• BCM Search Launcher
• The BioSCAN Project
• Biologists's Control Panel
• Harvard Biological Laboratories
• Cambridge School of Biological Sciences
• DOE Biology Information Center
• The WWW Virtual Library: Biomolecules
• BNL Genome analysis
• Brookhaven National laboratory
• Welcome to ExPASy
• Biologists Search Palette
• Bio-wURLd
• Virtual Genome Center
• EERIE GENOME server
• Useful Web Sites for Molecular Biologists
• European Bioinformatics Institute (EBI)
• Welcome to MIPS
• BEN (Belgian EMBL Net Node)
• BEN's Anonymous FTP server
• BEN's SRS6 server
• WWW2GCG at BEN (Password is required)
• Infobiogen server France
• The Protein Research Foundation

TUTORIALS AND COURSES ON THE WEB

• NCBI Newsletter
• NCBI online Tutorials
• Bioactivity: a web practical in bioinformatics:
• Internet course on Biocomputing (10 weeks) at Bielefeld:
• Phylogenetic Analysis of Proteins (Fred Opperdoes)
• Introduction to Phylogeny

SOFTWARE FOR SEQUENCE ANALYSIS

• BEN's FTP server
  
• UNIX AND MAC OS X
  • BioApps/Emboss/Fasta/FastDnaML/NCBI Blast etc., on IUBIO
    • Info on how to install Emboss on Mac OS X
    • Staden Package for Mac OS X
    • EMBOSS at EBI
    • Search Luancher Batch Client at Baylors College, Texas
    • Darwin
    • NCBI's Cn3D
• MULTI-PLATFORM
  • FTP Directory: ftp://ftp.ncbi.nlm.nih.gov/sequin/
  • RasMol V2.7.2 Manual
  • Getting RasMol/UMass Amherst
  • RasMol V2.7.1.1 README
  • SeqPup biological sequence editor version 0.9 for Java
  • Chemscape Chime: download page
  • Molecular Tutorials using Chemscape Chime from MDL Information Systems
  • HIV-1 protease -- structure with indinavir
  • NCBI's Cn3D
    
• FOR PC ONLY
  • AcaClone pDRAW32 - Freeware DNA cloning, analysis and plotting (PC only, crosswinds)
  • AcaClone pDRAW32 - Freeware DNA cloning, analysis and plotting (PC only, Geocities)
  • AcaClone pDRAW32 - Freeware DNA cloning, analysis and plotting (PC only, Denmark)
  • CHROMAS download page (Technelysium Pty Ltd)
  • ISYS Software Homepage
  • BioEdit Sequence Alignment Editor for Windows 95/98/NT
  • GeneDoc HomePage
  • SeaView
  • SeqVerter (A sequence format converter)
  • GeneStudioPro
  • FORCON download page
  • The online ForCon manual
  • Molecular Evolutionary Genetics Analysis MEGA
  • TREECON download page
    
• FOR MACINTOSH
  • NCBI's Cn3D

  PHYLOGENY

  • Joe Felsenstein's Phylogeny programs website
  • Phylogenetic Analysis Computer Programs
  • 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) PC only
  • Phylogeny server at Pasteur
  • SOAP Stability of aligned positions
  • TreeEdit
  • Treeview
  • FORCON download page (sequence format interconversion for PC only)
  • Mesquite