Fickette, the person who invented testcode analysis, suggested
a framework for gene finding:
- Regulatory and protein coding regions are unlikely to
occur in the repeats.
- Sequence similarities to other genes or gene products
provides strong positive evidence for exons.
- Codon bias over a region is one of the clearest
indicators of protein coding regions.
- The existence of patterns, such as TATA box, may indicate
Hints: to continue the project, you may want to do the
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.
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
Please send your repeats output result and POST to FTP to
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
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.
Send the codon frequency table you made (x.cod)
to FTP to (x
= your group number)
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.
Send your POST
that record your assignments to FTP to