[Biopython-dev] GenBank alphabet

Brad Chapman chapmanb at arches.uga.edu
Sun Nov 24 15:55:21 EST 2002


> what's the relation between an entry alphabet and its sequence?
> Case in point: Tests/cor6_6.gb, first entry.
> ATCOR66M is a mRNA, but the sequence is a DNA one (as documented by the 
> NCBI).  So:

Good point. I think this is something else I jacked up (what's new? :-).
The sequence itself is DNA, so they should actually probably use cDNA to
be "correct" about it. I never even thought about this.

> * what do biologists prefer?

We don't care :-). Seriously, this should be DNA 'cause it has Ts and
not Us.

> * what to store in a BioSQL record (BioPerl says dna)?

Also DNA. We have to be consistent with the actual content of the
string; the origin of the sequence as an mRNA should be stored somewhere
else (presumedly) in the GenBank record. Also good to be consistent with
BioPerl 'cause those guys are always right.

I fixed this in CVS. Thanks for pointing it out.


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