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

	Tools
		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  Miscellaneous: Check out browser colors Hoax info: is it a virus ir a joke? Search the Net Stroud's Win9x applications
		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  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
	Links
		(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 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
		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)
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