codon usage - (Mar/18/2009 )

i'd like to compare the codon in my cloned gene to the prefered codon usage in yarrowia, how can i do this, i checked some online website or software, but i still have no idea how to use them. people who has experience on this aspect, please help me and give me some advices. thank you.my email:yyanglf@hotmail.com

lufang on Mar 18 2009, 07:28 AM said:

The output from these programs will show you the frequency of each codon in RNA products from your genome of interest. You need to ensure that the codons being used in your gene are among those frequently used by the organism. If you have codons in your gene of interest that are infrequently used, particularly if there are several in a row, translational problems may occur.

i have problem in how to use these online software.now i want to know how to use the CODONW from MOBYLE website. it's very different for me. could you please tell me which software is easier for the beginner like me.

lufang on Mar 18 2009, 09:48 AM said:

Try http://gcua.schoedl.de/, enter your sequence name, select the sequence species for your gene, then compare to your desired organism under the dropbox titled Codon usage table to apply (Saccharomyces, etc.). You will then be shown a graphical output which clearly shows your infrequently used codons.
Codon positions shown in grey or red may be of concern. If protein fragments are obtained, it is likely these positions may be acting as "termination" signals (not directly, but rather due to a lack of the proper codon availability).

Alternatively, choose "each codon vs. usage table" from the homepage, input the proper information as before and you can compare the frequency of all codons between 2 organisms for a particular gene or in general by selecting "compare two usage tables" from the homepage.

i tried this and i got the results. but i don't know how to get conclusion from these columns. anyway, thank you very much. now i know how to get these columns.