Workshop (III)

Fickette, the person who invented testcode analysis, suggested a framework for gene finding:

  1. Regulatory and protein coding regions are unlikely to occur in the repeats.
  2. Sequence similarities to other genes or gene products provides strong positive evidence for exons.
  3. Codon bias over a region is one of the clearest indicators of protein coding regions.
  4. The existence of patterns, such as TATA box, may indicate functional sites.

Hints: to continue the project, you may want to do the following things

  1. You have learned how to interprete the Blast results this morning. If you want to make a better assignment of your orf's, please modify your POST.
  2. You have also learned how to predict repeats and the get the results back. Let's analyze the Repeat results and see where the repeats are in your sequence. (Mark it on your GeneMark figure yourself)
  3. Please send your repeats output result and POST to FTP to
  4. Now you have the Blast results of all the orf's in your sequence. You also know where all the repeats are. Please make preliminary assignments based on the first two Fickette's criteriors and then calculate the codon frequency.
  5. Please compare your freq. table with the correct freq table (hp.cod) and write your comments in the first few lines of this file using notepad.
  6. Send the codon frequency table you made (x.cod) to FTP to (x = your group number)
  7. Please determine which orf's could be real on the basis of the correct codon frequency table (hp.cod) you obtained from workshop3 Record your assignments in POST.
  8. Send your POST that record your assignments to FTP to