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

Peter Cock p.j.a.cock at googlemail.com
Fri Aug 30 15:46:59 UTC 2013

Who are our sequence mass experts?

---------- 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?
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?

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