[BioPython] [DETECTED AS SPAM] Re: back-translation method for Seq object?

[Leighton Pritchard]

On 22/10/2008 16:04, "Bruce Southey" <bsouthey at gmail.com> wrote:

> Peter wrote:
>> On Wed, Oct 22, 2008 at 9:31 AM, Leighton Pritchard <lpritc at scri.ac.uk>
>> wrote:
>>   
>>> On 21/10/2008 21:36, "Bruce Southey" <bsouthey at gmail.com> wrote:
   
>>>> For completeness as these are not 100% correct,
>>>> Leu/L =(TTA|TTG|CTT|CTC|CTA|CTG) = (TTN|CTR) = YTN
>>>> Arg/R =(CGT|CGC|CGA|CGG|AGA|AGG) =(CGV | AGR) = MGV
>>>> Ser/S =(TCT|TCC|TCA|TCG|AGT|AGC) =(TCN|AGY) = WSN
>>>>       
>> 
>> I was going to jump up and down and disagree with you here Bruce, but
>> Leighton has already made the same point, (CGV | AGR) != MGV etc.
>> It is true that the ambiguous codon MGV would cover all the possible
>> Arg codons, but it includes more than that.
>>   
> Leighton does show these are correct:
> (CGV | AGR) == MGV
> and MGV ==(CGV | AGR)

I showed (and Peter also points out) that (TTN|CTR) is a subset of YTN, and
that (TCN|AGY) is a subset of WSN, and not that they are equivalent, which
is what you have written above.  For that equivalence, we would also require
that MGV is a subset of (CGV|AGR), which is not true.

Likewise I also showed that, although (CGV|AGR) is a subset of MGV, neither
CGV nor MGV include CGT, which is a valid codon for arginine.  Whether or
not this error is corrected to CGN/MGN, the regular expression is still only
a subset of those codons implied by the IUPAC ambiguity symbols.

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


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