[Biopython-dev] [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq)

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2381





------- Comment #52 from lpritc at scri.sari.ac.uk  2008-11-07 04:48 EST -------
(In reply to comment #50)

> The use of 'cds' alone is wrong because cds refer to DNA not translation and
> not to protein sequences. The use of cds is confusing or at least vague until
> you determine how it works. 

I think that translate() also refers only to nucleotide sequences, and
therefore the association of 'cds' is not inherently confusing on that count. 
I think that it can be an appropriate term in an argument name (see above).

> Also it could be wrong in the sense it is a valid
> cds (see the GUG initiation in mammalian NAT1 example at the NCBI link) just
> not allowed by the table in Bio.Data.CodonTable.

It's up to the user to use the correct codon table for their purpose, I think. 
Otherwise, how would you propose to correct for their error?

> [...] 'cds_start' [...] One interpretation that also
> comes to mind is that it is the location of the start of the cds in the
> sequence (cds start at...).

I agree with this.  It has the potential to be confusing.

> This is not a check that it is the start of a cds
> rather it is a check for a possible open reading frame (as not all open reading
> frames are cds).  

It is true that not all ORFs are CDS (indeed, by far the majority are not). 
However, open reading frames do not have to start with - or even contain - a
start codon.  They just do not contain an in-frame stop codon.  We've been over
this definition before (comment #21).

L.


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