piwik-script

Deutsch
    Chair of Bioinformatics

    Hot Links, Media and Outreach

    Hot Links

    Pubmed https://pubmed.ncbi.nlm.nih.gov/

    Alternativ, falls Pubmed nicht verfügbar: Europe PMC https://europepmc.org/

    Alignment/Stammbäume

    CLUSTALW/Clustal Omega https://www.ebi.ac.uk/Tools/msa/clustalo/

    MUSCLE https://www.ebi.ac.uk/Tools/msa/muscle/

    PHYLIP https://evolution.genetics.washington.edu/phylip.html

    Datensätze zu biologische Größen/Biotechnologie/synthetische Biologie

    BioNumbers https://bionumbers.hms.harvard.edu

    BioBricks https://biobricks.org/

    GoSynthetic https://gosyn.bioapps.biozentrum.uni-wuerzburg.de/index.php

    Dotplot

    Dotter https://sonnhammer.sbc.su.se/Dotter.html

    GEPARD https://mips.gsf.de/services/analysis/gepard

    JDotter https://athena.bioc.uvic.ca/virology-ca-tools/jdotter/

     

    Funktionsdatenbanken

    Functional Glycomics https://www.functionalglycomics.org/; https://ncfg.hms.harvard.edu/

    Gene Ontology https://www.geneontology.org

     

    Gehirn-Baupläne

    Blue Brain Projekt (EU) https://bluebrain.epfl.ch/

    Brain Activity Atlas https://www.brainactivityatlas.org/

    Brain Activity Projekt (USA) https://www.braininitiative.nih.gov/

    Connectome-Projekt https://www.openconnectomeproject.org

    Mouse Brain Connectivity Atlas https://mouse.brain-map.org/static/atlas

    Neuroaktivitätsdetektion https://www.ncbi.nlm.nih.gov/pubmed/23537512

    Temporal lobe https://www.temporal-lobe.com/background/connectome

    Virtual Insect Brain Lab https://www.neurofly.de/

    WormWiring https://wormwiring.org/

    Wurmatlas https://www.wormatlas.org/

     

    Genomannotation/Genannotation/Sequenzanalyse/Online-Bibliotheken/Experimetelle

    Datensätze

    BLAST https://blast.ncbi.nlm.nih.gov/Blast.cgi

    GenScan https://genes.mit.edu/GENSCAN.html

    RepeatMasker https://www.repeatmasker.org/

    ENCODE https://www.encodeproject.org

    Ensembl https://www.ensembl.org/Homo_sapiens/Info/Index

    GATK Workshop https://software.broadinstitute.org/gatk/guide/

    article?id=7869#1.3

    Genomic Science Program https://genomics.energy.gov

    Human Genome Project https://web.ornl.gov/sci/techresources/Human_Genome/

    index.shtml

    UCSC https://genome.ucsc.edu/

    DDBJ (DNA Data Bank of Japan) https://www.ddbj.nig.ac.jp/

    EBI https://www.ebi.ac.uk/services

    European Bioinformatics Institute (Portal), besonders gut für Bioinformatik: Bioperl, Biojava, Programm-Module

    iGEM Parts https://igem.org/Main_Page

    MEDLINE/NCBI/PubMed https://www.ncbi.nlm.nih.gov/pubmed/

    National Center of Biotechnology Information: Allgemeiner Einstieg, viele Datenbanken und Software (Portal)

    NIH https://www.genome.gov

    OMIM https://www.omim.org/

    Swiss Bioinformatics Institute (Portal mit dem Expert Protein Analysis System): https://www.sib.swiss/

    WebDirectory https://www.biologydir.com/over-population/p1.html

    Computational Population Biology https://compbio.cs.uic.edu/

    GENEVESTIGATOR https://genevestigator.com/gv/

    GEO https://www.ncbi.nlm.nih.gov/geo/

     

    Grafikprogramme, Modellierung und Netzwerkanalyse

    CellDesigner https://www.celldesigner.org/

    CellNetAnalyzer https://www2.mpi-magdeburg.mpg.de/projects/cna/cna.html

    Cytoscape https://www.cytoscape.org/

    COBRA https://opencobra.github.io/

    COPASI https://copasi.org/

    Flux balance analysis https://systemsbiology.ucsd.edu/Downloads/FluxBalanceAnalysis

    Jimena https://www.bioinfo.biozentrum.uni-wuerzburg.de/computing/jimena_c/

    MATLAB https://de.mathworks.com/products/matlab.html

    Metatool https://pinguin.biologie.uni-jena.de/bioinformatik/networks/metatool/

    Odefy https://www.helmholtz-muenchen.de/icb/software/odefy/index.html

    PLAS https://enzymology.fc.ul.pt/software/plas/

    PottersWheel https://www.potterswheel.de/Pages/

    SQUAD https://www.vital-it.ch/software/SQUAD

    YANA/YANAsquare https://www.bioinfo.biozentrum.uni-wuerzburg.de/computing/yanasquare/

     

    Interaktionsdatenbank, Medikamenten-Interaktionsdatenbank

    catRAPID https://s.tartaglialab.com/page/catrapid_group

    HPRD https://hprd.org/

    iHOP https://www.ihop-net.org/UniPub/iHOP/

    KEGG https://www.genome.jp/kegg/

    NPInter https://www.bioinfo.org/NPInter/

    PlateletWeb https://plateletweb.bioapps.biozentrum.uni-wuerzburg.de/plateletweb.php

    Roche Pathways https://biochemical-pathways.com/#/map/1

    STRING https://string-db.org

    DrumPID https://drumpid.bioapps.biozentrum.uni-wuerzburg.de/compounds/index.php

    STITCH https://stitch.embl.de/

    EcoCyc https://ecocyc.org/

     

    Lokalisations-/Motiv-Vorhersage

    LocP https://ekhidna2.biocenter.helsinki.fi/LOCP/

    LocSigDB https://genome.unmc.edu/LocSigDB/

    nucloc https://www.nucloc.org/

    NucPred https://www.sbc.su.se/~maccallr/nucpred/

    SignalP https://www.cbs.dtu.dk/services/SignalP/

    TMHMM https://www.cbs.dtu.dk/services/TMHMM/

    Functional Glycomics https://www.functionalglycomics.org/

    ELM https://elm.eu.org/

     

    Programmiersprachen

    Biojava https://biojava.org/

    BioPerl https://bioperl.org/

    C++ https://www.cplusplus.com/

    Java https://www.oracle.com/technetwork/java/index.html

    Perl https://www.perl.org/

    Python https://www.python.org/

    R https://cran.r-project.org/

    Bioconductor https://www.bioconductor.org/

     

    Promotoranalyse

    AIModules                           https://aimodules.heinzelab.de/#/

    ALGGEN PROMO

    https://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.

    cgi?dirDB=TF_8.3

    Genomatix https://www.genomatix.de/

    JASPAR https://jaspar.genereg.net/cgi-bin/jaspar_db.pl

    MotifMap https://motifmap.igb.uci.edu/

    TESS https://www.cbil.upenn.edu/tess/

    TRANSFAC https://www.gene-regulation.com/pub/databases.html

     

    Proteinanalyse

    AnDom

    https://andom.bioapps.biozentrum.uni-wuerzburg.de/index_new.

    html

    CATH https://www.cathdb.info/

    Conserved Domains https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

    ExPASy https://www.expasy.org

    InterPro https://www.ebi.ac.uk/interpro/

    MODELLER https://salilab.org/modeller/tutorial/

    PDB https://www.rcsb.org/pdb/home/home.do

    Pfam https://pfam.xfam.org/

    ProDom https://prodom.prabi.fr/prodom/current/html/home.php

    PRODORIC https://prodoric.tu-bs.de/

    PROSITE https://prosite.expasy.org

    PyMOL https://www.pymol.org/

    QUARK https://zhanglab.ccmb.med.umich.edu/QUARK/

    Ramachandran-Plot https://mordred.bioc.cam.ac.uk/~rapper/rampage.php

    RasMol https://www.openrasmol.org/

    SCOP (old) https://scop.mrc-lmb.cam.ac.uk/scop/

    SCOPe updated https://scop.berkeley.edu/

    SMART https://smart.embl-heidelberg.de/

    SWISS-MODEL https://swissmodel.expasy.org

    UniProt/Swiss-Prot https://www.uniprot.org/

     

    RNA-Analyse

    ITS2 https://its2.bioapps.biozentrum.uni-wuerzburg.de/

    LNCipedia https://www.lncipedia.org/

    mfold Webserver https://unafold.rna.albany.edu/?q=mfold/RNA-Folding-Form

    microRNA.org/miRanda https://www.microrna.org/microrna/home.do

    miRBase https://www.mirbase.org/

    regRNA https://regrna2.mbc.nctu.edu.tw/             (not working, use instead RFAM):

    Rfam https://rfam.xfam.org/

    Riboswitch-Finder https://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/

    RNAAnalyzer https://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/

    RNAfold Webserver https://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi

    TargetScan https://www.targetscan.org

    tRNAscan https://lowelab.ucsc.edu/tRNAscan-SE/

    Vienna Package https://www.tbi.univie.ac.at/RNA/

    Media and Outreach

    "Bioinformatik" (Dandekar and Kunz, second edition WS 2021, english edition SS 2023)

    "Regulatory RNA" (Dandekar and Sharma, 1998)

    "RNA Motifs and Regulatory Elements" (Dandekar, ed.; Dandekar, Bengert, Ostareck and Ostareck-Lederer, 2002)

    "Auxins and Cytokinins in Plant Biology" (Dandekar and Naseem, 2017)

     

    Sendung "Retten Super-Pflanzen unser Klima?" am 17.06.2020 bei "nano" in 3Sat
    (Link zur Mediathek: https://www.3sat.de/wissen/nano/200617-co2-absorber-genpflanzen-mit-klimaturbo-100.html)

    Sendung "Bioinformatik" am 13.02.2014 bei "Scobel" in 3sat