Bioperl: article for Dr. Dobb's Journal

[francis@ncbi.nlm.nih.gov]

> From: Gustavo Glusman <bmgustav@bioinformatics.weizmann.ac.il>

> * "Otherwise, we quickly transcribe the sequence to RNA using Perl's tr()
> operator (which actually stands for "translate", not "transcribe") and
> return the sequence in RNA form."
> -> As a biologist I agree, this is perfectly kosher, but is the kind of
> things that inflates the text. For the typical DDJ reader, it would have
> been as good to write "otherwise, we quickly translate the sequence to RNA
> form using the tr() operator". We're not talking about translating a DNA
> molecule into RNA, but about translating its sequence in silico...

I disagree ... as a biologist who hangs out with lots of computer
folks, I know this is a tough one, and I think it is a mistake to cut
biology corners to make more computer sense ... We are not doing anybody
a favor by doing so. (even saying "translating its sequence in silico"
can lead to confusion when you are doing a translation using a gc table).

Biology is not always simple, and the data model we are presenting
(Lincoln is presenting) is a simplification of what life is (that's why
it's a model :-), but simplifying too much defeats the purpouse ...
imho.

---

I haven't finish reading the whole article (in the packing boxes right
now), but I hope to send Lincoln some suggestions soon.

cheers,

f.

--
| B.F. Francis Ouellette             
|
| francis@ncbi.nlm.nih.gov   

New Address: francis@cmmt.ubc.ca



 
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