Addresses used in this course

Databases and Database Searches

• BLAST
• Brookhaven Protein Database
• EMBL
• Entrez
• PROSITE
• SwissProt
• FASTA
• PROTEIN MACHINE
• DARWIN
• PSORT
• GenBank
• PIR
• Enzyme
• Pfam
• Blocks
• NLR-3D
• BLOCKS
• OWL
• PRINTS
• Seqnet
• Organelle Database
• Prodom
• WIT
• rRNA database project

Multple alignment

• PredictProtein
• BOXSHADE
• Multalign
• ClustalW server at the Baylor College in Houston
• Readseq server at the NIH

http://www.icp.ucl.ac.be/~opperd/protein_course/proteins.html

Belgian EMBL node computer (BEN)

Programs and software

• Puzzle
• ClustalW
• ProtML
• BLAST algorithms
• Neighbor of the Phylip package (Jo Felsentein, Univ. Washington),
• ClustalW (D. Higgins, EMBL) ,
• Distnj in the Protml package (Adachi and Hasegawa, Univ. Tokyo)

http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

ftp://rdp.life.uiuc.edu/rdp/programs/TreeTool

Tree of Life web page

Genome projects and databases

• Saccharomyces Genome Database
• Saccharomyces Genome Database
• Mycoplasma genitalium database
• Haemophilus influenzae database
• Methanococcus jannaschii database
• E. coli genome center
• Heliobacter pylori database
• E. coli database collection
• Sanger Center C. elegans homepage
• Bacillus subtilis database
• Genome Sequencing Center, St. Louis
• Methanobacterium thermoautotrophicum abstract
• The Genome Database
• Sanger Center S. pombe homepage
• Human Genome Project Infor
• Mouse Genome Databasemation
• Arabidopsis thaliana Database at Stanford
• Flybase
• Drosophila database
• TIGR Arabidopsis thaliana Database
• Fiocruz T.cruzi Genome Project
• Leishmania Genome Network, Seattle, USA
• Parasite genomes databasesWHO Leishmania Genome Network Web site
• Pyrococcus furiosus news article
• Pyrobaculum aerophilum abstract
• MycDBMycobacterium tuberculosis Genome Project
• Mycobacterium leprae Genome Project
• Mycoplasma Genome Project
• Borrelia burgdorferi news article

http://www.ncbi.nlm.nih.gov/

http://www.ebi.ac.uk/subs/emblsubs.html

http://www3.ncbi.nlm.nih.gov/Bankit/index.html

http://www.ebi.ac.uk/

• 'Bioactivity' - a web practical in bioinformatics: http://www.biochem.ucl.ac.uk/bsm/dbbrowser/jj/
• Internet course on Biocomputing (10 weeks): http://www.techfak.uni-bielefeld.de/bcd/welcome.html

The World Wide Web Virtual Library - Biomolecules: http://golgi.harvard.edu/sequences.html

The databases available on the BEN computer.