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CODONPREFERENCE program

Chris Barry chbarry at mackiller.llnl.gov
Tue Apr 23 13:29:58 EST 1996


Chris Barry wrote:
> 
> Hello,
>     I have been using the CODONPREFERENCE and FRAME programs of GCG to
> determine the open reading frames and the start codons. Unfortunately,
> in the graphical output, it does not give the exact 3 base location of
> the start/stop codons. I have tried using a text editor of the output
> files to see if they would give me some clue... they were not obvious.
> Is there a way to determine these locations easily? Any advice would be
> greatly appreciated. Thanks in advance.
> 
> Chris

I thought I would share this solution to my problem if any of you are
interested. 

1)Create a text file with these three lines in it

	pattern file start_codon
	..
	Start_C 1 ATG 0

2)Save as start_codon.dat
3)run map in WPI using start_codon.dat as the enzyme data file instead
of the default dat file.
4)the output should give the locations of the start codons



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