Unknown DNA — Rational Primer Design and Analysis — the ...

CodonFrequency to create a custom table for my example dataset that combined Giardia, Dictyostelium, and
Physarum preexisting tables.
Now go to the “Functions” “Translation” “BackTranslate” menu and specify the “Selected region” in the
“Which selection” window. In the BackTranslate program window change the “Would you like to see:”
default to “table of back-translations and the most probable sequence.” You also need to change the
“Codon Frequency Table . . .” from the default “ecohigh.cod” to something more reasonable, so press the
button and choose either the human, maize, or yeast table, whichever is the most appropriate for your project
system, from the “Chooser for Codon Frequency Table” window that pops up. Press the “OK” button in the
“Chooser” window after selecting the appropriate table. Here’s my run setup for BackTranslate:
Press “Run” in the program window when you’ve gotten your settings correct. The output will quickly be
displayed; notice how each amino acid residue’s codon choices are listed as a frequency. My abridged
upstream elongation factor backtranslation sequence data file is shown below:
!!NA_SEQUENCE 1.0
BACKTRANSLATE of: : input_8.rsf{BSC5936.week3} check: 5546 from: 9 to: 38
/////////////////////////////////////////////////////////////////////////////////
Thr His Ile Asn Leu Val Val
ACT 0.30 CAC 0.52 ATT 0.44 AAT 0.50 CTC 0.27 GTT 0.35 GTT 0.35
ACC 0.28 CAT 0.48 ATC 0.41 AAC 0.50 TTA 0.24 GTC 0.31 GTC 0.31
ACA 0.25 ATA 0.15 CTT 0.19 GTG 0.20 GTG 0.20
ACG 0.16 TTG 0.13 GTA 0.14 GTA 0.14
CTG 0.12
CTA 0.05
34 31 21 17 15 22 32
16 - 22
18