[BioPython] Transcription

[Ann Loraine]

Hello,

I guess the "translate" functions are more useful. I've used biopython
tools many times to translate nucleotide sequences into proteins,
using different genetic codes. It is a very useful feature, often the
first step in series of computations.

Maybe the audience was responding to how we programmers like to
represent biological sequences as character strings? DNA, the
molecule, is double-stranded, so it might be more proper to model it
as a pair of strings. But this would be wasteful of space, since one
string is all you need to capture the sequence of both strands.

They are right that the antisense strand is used as the template for
RNA synthesis (transcription), but I'm not sure if it is proper to say
that one strand or the other is being transcribed. Maybe in future you
could say something like: biopython sequence objects have a string
that represents a sequence of nucleotides, and when you call a
transcribe method, the method assumes that this string also represents
the sense strand of a double-stranded DNA molecule.

Best wishes,

Ann




On 7/10/07, Michael Fahy <fahy at chapman.edu> wrote:
> I just showed the BioPython tutorial to some of our Biology and Chemistry
> faculty.  They pointed out that all the "Transcribe" function does is
> replace each occurrence of "T" in the sequence with a "U".  The biologists
> said that that is not what they mean by transcription.  They felt that each
> nucleotide should have been replaced by the complementary nucleotide, and
> that the resulting string should have been reversed.
>
> This, they said, would be concordant with the way in which biologists use
> the term "transcribe'.  It would not be hard to do, so why does BioPython do
> what it does and call it transcription?
>
>
>
>
>
> Michael Fahy
>
> Mathematics and Computer Science
>
> Chapman University
>
> One University Drive
>
> Orange, CA  92866
>
> (714) 997-6879
>
> fahy at chapman.edu
>
>
>
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-- 
Ann Loraine
Assistant Professor
University of Alabama at Birmingham
http://www.transvar.org
205-996-4155