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

Books? I'm not sure. For basic knowledge, Wikipedia is actually quite
good. For methods, openwetware.org is great, but most of the protocols
are written by people with enough resources that they never question
their methods; often, their methods are unnecessarily difficult, or
inefficient, or a waste of resources, so copying them may waste your
time/money/efforts.

For software, I'm not really sure. I'm not yet sure I can endorse
PySplicer (my first PySplicer-designed gene is on its way as we speak, I
hope..), but I'm not sure what else to endorse, either; as I said, many
tools use outdated methods but I haven't checked which one uses which,
or which is reliable. Some companies offer to do gene optimisation for
you for free, and they will probably know more than you about the
process, so perhaps just trust them to do it right?

Are you academically affiliated? If not, iGEM want nothing to do with
you. So if you want to take part, find an academic lab to work with
soon, and start raising the pretty big fee you'll be required to pay...

...or take part in goodiybio.org for free! :)

On 27/10/12 17:58, shreyans chordia wrote:
> Your tips are very helpful.. thank you : )
> Actually, right now I'm just researching all the tools used in synbio and
> hunting for new project ideas. I wish to compete in the iGEM next year..
> Could you suggest me some books for researching the tools, or maybe a short
> list of very important tools useful for gene and protein optimization that
> i can look-up..
>
> Regards,
> Shreyans
>
> PS:
> all the best with the future versions of PySplicer
>
> On Thursday, 25 October 2012 20:14:21 UTC+2, Cathal wrote:
>>
>> 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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