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Useful Tools and Links
Not exclusively for biologists !
Last major update: 15.11.05 (SR)

tools-Logo   Tools

search-Logo    

 General Info / Tools
"Local" stuff:
EFA BW - Fahrplanauskunft
Kleinanzeigen: Schnapp
Kleinanzeigen: Zypresse
Postleitzahlen (city codes)
Regionalwetter nach Postleitzahl
Telefonbücher (phone books)
Secure WEBMAIL (biologie.uni-freiburg.de)
Travelling:
Currency calculator
Deutsche Bahn - connection query
LCC24 - flight booking
Mapblast: Draw maps from any location
Route planning via web.de portal
Weather: Meteomedia Messnetz chili-Logo
Miscellaneous:
Check out browser colors
Hoax info: is it a virus ir a joke?
Search the Net
Stroud's Win9x applications


biostuff-Logo   Online Bio Tools
Alignment:
  • Boxshade: Color your alignment
  • ClustalW multiple sequence alignment at the EBI
  • MUSCLE
  • ProbCons multiple sequence alignment at Stanford
  • Literature search:
  • e-journals (biology, UB Freiburg)
  • Navigator Elektronische Publikationen UB Freiburg
  • ReDI BW
  • Pubmed (NCBI)
  • GoPubMed: combines PubMed queries with GO terms
  • Google Scholar
  • Scopus
  • NCBI:
  • BLAST search
  • Entrez meta browser
  • Taxonomy browser
  • Phylogenetic footprinting (promoter analysis):
  • CONREAL
  • ConSite
  • Footprinter
  • Monkey
  • PLACE
  • Proteomics / structure:
  • BIND: Biomolecular Interaction Network
  • ExPASy Proteomics Tools
  • FUGUE search against HOMSTRAD (structure search)
  • HMMSTR ab initio protein structure prediction using homology 
  • InterPreTS: interaction prediction
  • PDB protein substructure visualization
  • PPG: makes nice 3D protein images for publications
  • protein structure data mining
  • STRING: Search Tool for the Retrieval of Interacting Genes/Proteins
  • WebPACADE protein structure search
  • RNA / RNAi / miRNA / siRNA:
  • BIOPREDsi: predicts siRNA sequences with optimal knockdown effect
  • dsCheck: off-target search for dsRNA-mediated RNAi
  • E-RNAi: design of RNAi constructs
  • microInspector: detection of miRNA binding sites
  • miRU: plant microRNA target finder
  • SFOLD: RNA folding and design
  • MFOLD: RNA folding
  • Vienna RNA secondary structure prediction
  • Subcellular localization / targeting:
  • MultiLoc / TargetLoc
  • SherLoc: including literature information chili-Logo
  • PA-SUB (protein sorting prediction)
  • PSORT (protein sorting prediction)
  • Signal sequence / gene prediction @ CBS
  • TargetP: prediction of subcellular location (includes ChloroP)
  • TMHMM: prediction of transmembrane alpha helices
  • TMBETA-NET: prediction of transmembrane beta strands
  • TMB-HUNT: prediction of transmembrane barrels
  • Miscellaneous:
    EMBL online sequence submission and EMBL feature description
    FASTA format and IUPAC code (@ NCBI)
    MG align: alignment of cDNA vs. genomic DNA
    pattern discovery @ IBM life sciences
    Primer Design (Primer3)
    Sequence analysis @ uhura chili-Logo

    links-Logo   Links

    db-Logo 
     (Sequence) Databases
    Comparative Genomics:
    DOE Joint Genome Institute
    ENSEMBL Genome Browser
    GOLD: Genomes OnLine Database
    NCBI Genome Browser
    PlantGDB: Resources for plant comparative genomics
    The New York Plant Genomics Consortium
    Sputnik EST clustering
    TIGR Gene Indices
    Gene Ontology (GO):
    AmigGO GO Browser
    Gene Ontology home
    QuickGo GO Browser (EBI)
    Microarrays:
    Gene Expression Omnibus (NCBI)
    Genevestigator: Arabidopsis array data
    Cluster analysis and visualization
    Nucleic Acids:
    Eukaryotic Promoter Database (EPD)
    Genbank
    NCBI:
  • cluster of orthologous groups (COG)
  • non-redundant EST clusters (Unigene)
  • RefSeq: non-redundant set of sequences for major research organisms
  • trace archive (genomes under way)
  • Organisms:
    TAIR Arabidopsis database
    Arabidopsis Gene Farm
    ChlamyDB (Chlamydomonas)
    Cosmoss.org and PHYSCObase (moss)
    Cyanobase (Synechocystis db)
    Proteins:
    CATH database of structural domains
    Database of interacting proteins (DIP)
    Interpro (motifs)
    PFAM protein family database
    Prosite (motifs)
    Swissprot
    Uniprot and the ID tracker
    Repeats:
    Arabidopsis repbase (repeats)
    GIRI Repbase (repeats)
    TIGR Plant repeat database
    Miscellaneous:
    Bryophyte collection database
    KEGG (pathways and compounds)
    Plant C-value database (Kew Botanic Garden)
    REBASE (restriction enzymes)
    RFAM (RNA families)
    SRS (keyword search)


    bioinformatics logo 
    Bioinformatics
    Bioinformatik in Freiburg 
    bioinformatik.de link page
    BioTech at Indiana University
    Editorial 'Bioinformatics'
    EMBL's EBI outstation
    EMBOSS
    ExPASy server
    MGALIGN (cDNA vs. genomic)
    Multiple sequence alignment: Probcons and Muscle
    Nanotechnology / Nanogenes
    NCBI
    Pathwayexplorer: visualization of array data on pathways
    PEDANT software (genome analysis)
    Phylogeny Software
    Phylodome: visualize/analyze phylogenetic distribution of domains
    REPuter / REPuterVMATCH
    The Staden package
    The GCG Web interface W2H
    TREE-PUZZLE (ML phylogenetic software)
    TreeSimplifier
    UTR home
    Vienna RNA package
    FTP to FramePlus



    company-Logo  Companies and Organisations
    AgBiotechNet
    AgBioWorld
    ASK Software Shop
    BASF AG
    DENIC (.de)
    European Federation of Biotechnology
    DFG Schwerpunkt: Molekulare Analyse der Phytohormonwirkung
    Federation of European Societies of Plant Physiology
    Forschungsförderung Biotechnologie
    greenovation
    IAB - International Association of Bryologists
    INTERNIC (.com, .org, .net)
    IBM life sciences
    Informationssekretariat Biotechnologie
    ISPMB (International Society for Plant Molecular Biology)
    Plant Systems Biology, Ghent
    Pyramid Computer
    SUN Microsystems
    SuSE (Linux)
    Technelysium (Chromas)
    TLB (Technologie-Lizenz-Büro)



    books-Logo 
    Dictionaries
    Life Sciences
    List of Dictionaries
    QuickDic German<->English
    Scientific Quotations
    TU Chemnitz German<->English chili-Logo



    sports-Logo  (local) sports
    Bundesliga
    DSV
    EHC Freiburg
    FIS
    SC Freiburg
    SVS alpin



    recreation-Logo  Recreation etc.
    Cinema etc. by ticket
    Erdsicht: the earth from above and Google Earth
    Feldberg livecams
    Mandelbrot Applet by SUN
    Funny names
    Mensa-Speiseplan Vorderhaus KFH
    Pitztaler Gletscher
    Plant Biotech Cinema
    SETI@home screen blanker Distributed Computing
    Star Wars
    The Space Store
    ThinkGeek
    TV cult(ure)
    The Whitehouse.org patriot test!