I'm working on a project involving gene transcription and translation rates in Klebsiella pneumoniae and Acinetobacter baumannii. Is there a codon optimization tool for non-model organisms? Most of the tools I see (e.g. IDT, Benchling, etc.) only optimize for model organisms without the option for custom optimizations using a reference genome for the target organism.
1. This may be helpful for you.
https://support.geneious.com/hc/en-us/articles/360007150452-How-do-I-create-a-custom-codon-usage-table-
2. You should try Jcat ( http://www.jcat.de/ ) and ExpOptimizer ( https://www.novoprolabs.com/tools/codon-optimization ).
This seems to work:
Go to website http://www.geneius.de/GENEius/Security_login.action
Login to GENEius as a guest (username = User, password = GENEius)
Paste in an amino acid sequence (it says you can use a nucleic acid sequence, but I can't get that to work).
Click "analyse sequence", and then click "continue". You now need to get the codon usage table for your organism.
Go to http://www.kazusa.or.jp/codon/ and find the codon usage table you wish to use.
For K. pneumoniae go to http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=574
For A. baumannii use http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=400667
As an example, to do a K. pneumoniae optimization select this:
UUU 21.4( 9374) UCU 7.9( 3469) UAU 17.3( 7601) UGU 4.2( 1843)
UUC 15.6( 6841) UCC 10.1( 4430) UAC 13.2( 5790) UGC 6.7( 2945)
UUA 12.3( 5376) UCA 9.1( 3979) UAA 1.9( 838) UGA 1.0( 441)
UUG 12.8( 5588) UCG 9.4( 4112) UAG 0.5( 232) UGG 16.3( 7157)
CUU 14.7( 6445) CCU 8.0( 3495) CAU 11.9( 5192) CGU 13.3( 5841)
CUC 12.5( 5471) CCC 7.8( 3425) CAC 9.9( 4334) CGC 23.4( 10270)
CUA 6.0( 2628) CCA 7.9( 3475) CAA 13.1( 5751) CGA 6.1( 2676)
CUG 47.6( 20871) CCG 20.8( 9098) CAG 28.5( 12496) CGG 10.6( 4642)
AUU 24.7( 10841) ACU 9.0( 3934) AAU 18.8( 8255) AGU 8.9( 3918)
AUC 24.6( 10771) ACC 23.9( 10479) AAC 18.1( 7920) AGC 18.6( 8135)
AUA 9.1( 4004) ACA 9.2( 4020) AAA 29.4( 12870) AGA 4.9( 2165)
AUG 25.5( 11176) ACG 13.1( 5740) AAG 16.6( 7255) AGG 3.7( 1621)
GUU 16.9( 7406) GCU 15.9( 6968) GAU 29.9( 13100) GGU 17.2( 7555)
GUC 17.1( 7499) GCC 34.0( 14905) GAC 21.1( 9227) GGC 29.3( 12858)
GUA 10.8( 4749) GCA 17.1( 7511) GAA 30.9( 13519) GGA 11.5( 5052)
GUG 22.3( 9777) GCG 28.5( 12486) GAG 24.5( 10736) GGG 12.6( 5531)
Paste this into the text box in GENEius. Click "analyse codon usage". You then click "continue".
You then click on sequences to avoid (e.g. if you want your optimised sequnce to contain no EcoRI or HindIII sites, just select those two sites and they will appear in the "Current Selection" column). If this is of no interest, just click "continue".
Next you get a summary of your data, copy if you want a record of your selections, and then click "Start Optimisation". After a brief pause for calculations the results will appear.
Hope this is of use.
Regards,
Vince
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