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Home > Extras > Bioinformatics For Dummies® Bonus Material
Bioinformatics For Dummies® Bonus Material
By: Jean-Michel Claverie Ph.D., Cedric Notredame Ph.D.
 

[Bio FD Home][Ch.1][Ch.2][Ch.3][Ch.4][Ch.5][Ch.6][Ch.7][Ch.8][Ch.9][Ch.10][Ch.11][Ch.12][Ch.13][Ch.15]

Chapter 15: Some Useful Bioinformatics Resources

Ten important bioinformatics databases

Name URL Description
GenBank/DDBJ/EMBL www.ncbi.nlm.nih.gov Nucleotide sequences
Ensembl www.ensembl.org Human/mouse genome
PubMed www.ncbi.nlm.nih.gov Literature references
NR www.ncbi.nlm.nih.gov Protein sequences
SWISS-PROT www.expasy.ch Protein sequences
InterPro www.ebi.ac.uk Protein domains
OMIM www.ncbi.nlm.nih.gov Genetic diseases
Enzymes www.chem.qmul.ac.uk Enzymes
PDB www.rcsb.org/pdb/ Protein structures
KEGG www.genome.ad.jp Metabolic pathways

Twelve important software programs in bioinformatics

Category Name URL Description
Database Search SRS srs.ebi.ac.uk Database search (Chapter 4)
  Entrez www.ncbi.nlm.nih.gov Database search (Chapter 3)
  BLAST www.ncbi.nlm.nih.gov Homology search (Chapter 7)
  DALI www.ebi.ac.uk Structure database search (Chapter 11)
Multiple alignment ClustalW www.ebi.ac.uk Multiple sequence alignment (Chapter 9)
  Tcoffee igs-server.cnrs-mrs.fr/Tcoffee/ Multiple Sequence Alignment (Chapter 9)
Prediction GenScan genes.mit.edu Gene prediction (Chapter 5)
  PredictProtein cubic.bioc.columbia.edu Protein structure prediction (Chapter 11)
  Mfold www.bioinfo.rpi.edu RNA structure prediction (Chapter 12)
Phylogenetics Phylip bioweb.pasteur.fr/intro-uk.html Tree reconstruction (Chapter 13)
Editing/Visualization Jalview www.es.embnet.org Alignment editor (Chapter 10)
  Rasmol www.bernstein-plus-sons.com/software/rasmol/ Structure visualization (Chapter 11)

Ten bioinformatics resource locators

Name URL Description
ExPASy www.expasy.ch Dedicated to proteins
ArrayExpress www.ebi.ac.uk/microarray/ DNA chips
Swbic www.swbic.org Miscellaneous links
Pasteur bioweb.pasteur.fr/intro-uk.html Miscellaneous links; many online tools
RNA World www.imb-jena.de/RNA.html RNA-related links
Phylip evolution.genetics.washington.edu/ Everything on phylogeny
NCBI primers www.ncbi.nlm.nih.gov/education Very good primers on many subjects
Bielefeld bibiserv.techfak.uni-bielefeld.de/intro/dist.html Awesome online course
Bio-informer www.ebi.ac.uk/Information/News/ The EBI online news
Coffee Corner www.ncbi.nlm.nih.gov Online protein news

 

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