[Biojava-l] Regarding the transcription script

[Peter Cock]

On Wed, May 29, 2013 at 6:42 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> And the third sentence from that article is:  "during transcription, a DNA
> sequence is read by an RNA polymerase, which produces a *complementary*,
> antiparallel RNA strand."
>
> mRNA is complementary to the *non-coding* strand. If the original sequence
> is coding, you just change T and U. If not, you must make a complement
> containing U.
>
> The example sequence is clearly coding, thus the confusion.
>
> -da

Hi Christina and all,

This has come up on the Biopython mailing list a few times too.
Does the strand section in the Biopython tutorial help at all?

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc24

"Before talking about transcription, I want to try and clarify the
strand issue. Consider the following (made up) stretch of double
stranded DNA which encodes a short peptide: ...
The actual biological transcription process works from the
template strand, doing a reverse complement (TCAG -> CUGA)
to give the mRNA. However, in Biopython and bioinformatics
in general, we typically work directly with the coding strand
because this means we can get the mRNA sequence just
by switching T -> U."

Regards,

Peter