Re: [DIYbio] Re: Translating bacterial DNA into plant DNA

Many companies will do "mutagenesis" for cheap or even free during
synthesis of your DNA: for them, it technically means less work, as the
synthesis process involves a lot of error correction to begin with.

So, provided you don't care about sequence precision (for example,
whether or not your sequence contains restriction sites X, Y or Z), you
could do a project with some mutagenesis baked in, and try a bunch of
mutant variants, or even a heterogenous mix of DNA, and just select the
best variant.

On 24/10/12 19:42, Patrik D'haeseleer wrote:
> In addition, there are some indications that codon usage may differ between
> different parts of the plant, e.g. because of differential expression of
> tRNA synthetases. So you might need to use a different codon profile to get
> optimal protein expression in seeds versus in the flower.
>
> I've talked to some people who actually do codon optimization for plant
> engineering, and this wasn't even on their radar yet. We still have a lot
> to learn about codon optimization in higher eukaryotes, so probably the
> best advice is to try a couple different encodings and see what works best
> - if you can afford that, of course...
>
> Patrik
>
> On Wednesday, October 24, 2012 7:45:46 AM UTC-7, Cathal wrote:
>>
>> There's codon optimisation, and then there's codon optimisation. I'd
>> advise doing some research into the tools you use before committing to one,
>> when there's money on the line!
>>
>> For example, most tools out there (which are free to use) are still using
>> the "best pick" method, where they try to use the most common codon as
>> often as possible, while avoiding all the other stuff you've forbidden in
>> the output. This can lead to saturation of the tRNA synthetases that have
>> to recharge the used tRNAs for those codons, which often leads to a
>> bottleneck, delays in translation, and potentially either low or absent
>> gene expression.
>>
>> In other words, in some (rare) cases, using this codon optimisation method
>> can actually make the gene not express, because your RNA overuses certain
>> codons that get depleted quickly.
>>
>> Newer methods, which may work better (but your research may dispute this,
>> it's a contentious area), try to "match" codon frequencies instead for the
>> target species, or for subsets of the target species' genes. So if a codon
>> is used 60% of the time in a codon usage table, the resulting gene will be
>> designed to use that codon 60% of the time as well.
>>
>> That's the format I used when designing PySplicer, but PySplicer is still
>> beta-quality software. For example, it doesn't yet verify that the
>> frequencies in the output match the desired frequency spread within a
>> defined margin, and it doesn't check that local areas of poor frequency
>> codons are absent, stuff like that. It's on my roadmap of desired
>> features.. :)
>>
>> Just saying: do your research to make sure your codon optimiser isn't
>> using outdated methods!
>>
>> On 23 October 2012 21:52, shreyans chordia <shreyans...@gmail.com<javascript:>
>>> wrote:
>>
>>> Thanks.. found them on wiki.. there are many here.. was wondering which
>>> one is accurate out of the lot..
>>>
>>>
>>> On Monday, 22 October 2012 15:27:30 UTC+2, Mega wrote:
>>>>
>>>>
>>>> If I remember correctly, wikipedia linked me to a codon bias adapter. It
>>>> was just a website wwhere you inserted the sequence and it threw out the
>>>> optimized code.
>>>>
>>>>
>>>> If you want, I can look it up how it was called.
>>>>
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>>
>>
>>
>> --
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