Contents of the Practical Course

By Fred R. Opperdoes

Time: 15 hours or two full days somewhere in November
Place: Computer classroom in the Central Library of the Faculty

• 1. 1. Demo tour on Internet: the available tools:
  • Surf theWWW,
  • Send an electronic mail message
  • Connect to a Usenet newsgroup
  • Connect to the gopher service at BEN,
  • Connect to the molecular biolology software file server at Indiana University
  • Connect to a server using telnet
  • Connect to a server using the file transfer protocol FTP

• 1.2. Accessing on-line databases
  • Connect to GenBank at NCBI
  • Connect to SwissProt at Expasy
  • Connect to the protein domain database Prodom
  • Conncet to the Blocks database
  • Connect to the Bookhaven protein database
  • Connect to them all and many more via SRS

• 1.3. Accessing some e-mail servers
  • Darwin AllAll server
  • Mowse server
  • BLAST / FASTA servers

• 2. Facilities on the Belgian EMB Network Node (BEN)
  • Tour of GCG package in command mode via a telnet session
  • Accessing the GCG package via the Web server
  • Current sequence awareness

• 3. Hands on :
  • Protein analysis project via the WWW only
  • Protein identification based on the mass of peptide fragments
  • Search for homologous proteins using BLAST
  • Creation of a protein multiple alignment on BEN
  • Search of homologous protein domains using PRODOM and BLOCKS www servers
  • 3-D structure prediction using DARWIN at ETHZ and PredictProtein at EMBL
  • Creation of 3-D images of protein structures from PDB coordinates using RasMol on the Macintosh
  • Creation of a phylogenetic tree using PHYLIP on the ICP SGI Iris Indigo

• 4. Molecular graphics demo using BIOSYM on the ICP SGI Iris Indigo

Back to Introduction