[Biopython-dev] Fwd: [biopython] Potential error in mass calculations for RNA/DNA? (#229)

[Markus Piotrowski]

Hi,

I prepared a bugfix for that:
https://github.com/MarkusPiotrowski/biopython/commit/fd8914f14d48c984a69b6e8227c679e3c67bd1eb

Summary:
Bugfix for DNA/RNA masses

In Bio.Data.IUPACData:
- corrected masses for monophosphate nucleotides in 
unambiguous_dna_weights
and unambiguous_rna_weights (most values where too high by a mass of 16 
Da)
- added two dictionaries with monoisotopic masses for monophosphate
nucleotides (monoisotopic_unambiguous_dna_weights and
monoisotopic_unambiguous_rna_weights)
- added average and monisotopic masses for selenocysteine and 
pyrrolysine in
protein_weights and monoisotopic_protein_weights

In Bio.SeqUtils.__init__:
Rewrote method molecular_weight to
- correct the calculation (sum masses of sequence elements and 
substract 18
Da for each formed bond)
- allow mass calculation for RNA and protein sequences
- allow mass calculation for double stranded nucleic acids


Am 2013-08-30 17:46, schrieb Peter Cock:
> Who are our sequence mass experts?
> https://github.com/biopython/biopython/issues/229
>
> ---------- Forwarded message ----------
> From: nruggero <notifications at github.com>
> Date: Thu, Aug 29, 2013 at 11:03 PM
> Subject: [biopython] Potential error in mass calculations for 
> RNA/DNA?
> (#229)
> To: biopython/biopython <biopython at noreply.github.com>
>
>
> In Bio/Data/IUPACData.py the molecular weights of unambiguous DNA are
> listed as:
>
> unambiguous_dna_weights = {
>     "A": 347.,
>     "C": 323.,
>     "G": 363.,
>     "T": 322.,
>     }
>
> As far as I can tell these are the molecular weights for the 
> non-deoxy
> bases instead of the deoxy bases. For example, AMP (347.22) instead 
> of dAMP
> (331.22) is listed.
>
> I've looked at the original BioPearl code that these numbers were 
> taken
> from and I think they were just copied incorrectly. I have also 
> looked at
> the code which uses this dict in Bio/SeqUtils/__init__.py called
> molecular_weight() and it just takes the sum of these values over the
> sequence (no correction made).
>
> So, is this an error or am I missing something basic?
> Thanks
>
> —
> Reply to this email directly or view it on
> GitHub<https://github.com/biopython/biopython/issues/229>
> .
>
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