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Tutorial

  1. Go to the NCBI Web site with a web browser to collect protein sequences:
    http://www.ncbi.nlm.nih.gov/.
  2. Click proteins from the Search Box.
  3. Type the target gene name (`Bph') into the search for box.
  4. Click Go to start the search. Wait a little until the search is done.
  5. Click on the name of one interesting gene which is colored blue to select it as the starting gene.
  6. Copy the numeric part of the Genbank Index (GI) number. 
    Copy only the numbers of `gi|1073448' 
10173448
  7. Goto the BLAST search on NCBI.
  8. Select Basic BLAST search.
  9. Select Blastp (BLAST protein search of nr)
  10. Select Search by Accession or GI.
  11. Paste in the GI number and start the search.
  12. Click format results and the search result will show up on a browser new window.
  13. Print this page to file to save the output.
  14. Use the results to decide on how many sequences are similar enough to include together.
  15. Go back to the starting sequence
  16. Click Protein Neighbors from the Display Box.
  17. Click the Display button.
  18. Wait a little until the search is done and the results will show up on a new window.
  19. Click on the empty square boxes of interesting genes to select them. Use the Blastp results to decide on how many to select (up to 40).
  20. Click FASTA from the Display Box.
  21. The search result, FASTA format protein sequences, will show up in a new window.
  22. Click Save and save with the file extension `.fasta'. Repeat the procedure for other protein families. DEODAS can design oligos for multiple protein families as long as each family is in it's own `*.fasta' file.
  23. Open DEODAS program by running deodas.py & from a x-terminal and the DEODAS user interface will show up.
  24. Select the FASTA file directory. Oligonucleotides will be generated for each file ending `.fasta' in the directory.
  25. Select a codon usage table (see section Codon Usage table).
  26. Set the maximum subfamily dissimilarity (see section Maximum subfamily dissimilarity).
  27. Set the minimum oligonucleotide length (see section Minimum oligonucleotide length).
  28. Set the maximum mismatches (see section Maximum mismatches).
  29. Type in the names of the Genbank flat files to search (see section Genbank setting). .
  30. Either create a new results database or select an existing database (see section Results databases).
  31. Run the program by pressing OK (see section Running). The design process can take over a day so find something else to do. Additional design processes can be started with the interface as long as they are in different directories. The x-terminal running the design process will print messages and will print `Design process finished' when the process is finished.
  32. When the design process is finished click the query button to turn on deodasquery and analyze the results.
  33. Search the target descriptions by putting in single keywords by typing in the keyword and pressing enter.
  34. After finding an oligonucleotide matching a correct target in the Genbank databases search that oligonucleotide by name to check for incorrect matches to reduce the chance of cross-hybridization in the final oligonucleotides.
  35. When an oligonucleotide is selected for synthesis copy or type the name into the Select an oligonucleotide name box and press Enter.
  36. All selected oligonucleotides can be listed by clicking List Selections.
  37. The Print button prints everything in the results box.

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