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

[Leighton Pritchard]

On 17/10/2008 19:46, "Bruce Southey" <bsouthey at gmail.com> wrote:

> Leighton Pritchard wrote:
>> This is the key problem.  Forward translation is - for a given codon table -
>> a one-one mapping.  Reverse translation is (for many amino acids) one-many.
>> If the goal is to produce the coding sequence that actually encoded a
>> particular protein sequence, the problem is combinatorial and rapidly
>> becomes messy with increasing sequence length.
>>   
> If you use a regular expression or a tree structure then there is a
> one-one mapping but then that would probably best as a subclass of Seq.

I don't see this, I'm afraid.

Each codon -> one amino acid : one-one mapping
Arg -> set of 6 possible codons : one-many mapping

It doesn't matter how it's represented in code, the problem of a one-many
mapping still exists for amino acid -> codon translation in most cases.

The combinatorial nature of the overall problem can be illustrated by
considering the unlikely case of a protein that comprises 100 arginines.
The number of potential coding sequences is 6**100 = 6.5e77.  That you *can*
choose any one of these to be your potential coding sequence doesn't negate
the fact that there are still (6.5e77)-1 other possibilities... It doesn't
get much better if you use the the average number of codons per amino acid:
61/20 ~= 3.  A 100aa protein would typically have 3**100 ~= 5e47 potential
coding sequences.  I wouldn't want to guess which one was correct, and I
can't see a back_translate method in this instance doing more than producing
a nucleotide sequence that is potentially capable of producing the passed
protein sequence, but for which no claims can be made about biological
plausibility.

Now, a back_translate() that takes a protein sequence alignment and, when
passed the coding sequences for each component sequence, returns the
corresponding alignment of the nucleotide sequences, makes sense to me.  But
that's a discussion for Bio.Alignment objects...

> I would suggest tools like Wise2 and exonerate
> (http://www.ebi.ac.uk/~guy/exonerate/) are the solution to solving gene
> structure problems than using a Seq object.

I wouldn't suggest using a Seq object for this purpose, either... ;)

>> I agree - I can't think of an occasion where I might want to back-translate
>> a protein in this way that wouldn't better be handled by other means.  Not
>> that I'm the fount of all use-cases but, given the number of ways in which
>> one *could* back-translate, perhaps it would be better not to pick/guess at
>> any single one.
>>   
> Apart from the academic aspect, my main use is searching for protein
> motifs/domains, enzyme cleavage sites, finding very short combinations
> of amino acids and binding sites (I do not do this but it is the same)
> in DNA sequences especially genomic sequence. These are usually very
> small and, thus, unsuitable for most tools.

I do much the same, and haven't found a pressing use for back-translation,
yet - YMMV.

> One of my uses is with
> peptide identification and de novo sequencing using mass spectrometry
> when you don't know the actual protein or gene sequence. It also has the
> problem that certain amino acids have very similar mass so you would
> need to  Regardless of whether you use a regular expression query or not
> you still need a back translation of the protein query and probably the
> reverse complement.

Perhaps I'm being dense, but I don't see why that is.  Can you give an
example?

> Another case where it would be useful is that tools like TBLASTN gives
> protein alignments so you must open the DNA sequence and find the DNA
> region based on the protein alignment.

You could use TBLASTN output - which provides start and stop coordinates for
the match on the subject sequence - to extract this directly, without the
need for backtranslation.  Example output where subject coordinates give the
match location below:

>ref|NC_004547.2| Erwinia carotovora subsp. atroseptica SCRI1043, complete
genome
          Length = 5064019

 Score =  731 bits (1887), Expect = 0.0
 Identities = 363/376 (96%), Positives = 363/376 (96%)
 Frame = +3

Query: 1      MFHXXXXXXXXXXXXXTISVGMMAPFTFAEAKTPGTLVEKAPLDSKNGLMEAGEQYRIQY
60
              MFH             TISVGMMAPFTFAEAKTPGTLVEKAPLDSKNGLMEAGEQYRIQY
Sbjct: 477432 MFHLPKLKQKPLALLLTISVGMMAPFTFAEAKTPGTLVEKAPLDSKNGLMEAGEQYRIQY
477611

[...]

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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