Bioperl: article for Dr. Dobb's Journal
Sun, 11 Oct 1998 14:26:22 -0400
Gustavo Glusman writes:
> >I'm writing an article for Dr. Dobb's Journal on Perl and Molecular
> Reading it, a few comments -
> * Why talk about 21 amino acids, when there are 20? I can understand the
> expression 'the 21 letter alphabet', but a phrase like "The other thing to
> notice is that certain codons (three in all) don't encode any amino acids."
> certainly clashes with "the 21 amino acids"... Why not just talk about 20
> amino acids and 3 termination codes?
> * "For historical reasons, DNA subsequences use 1-based indexing,..."
> -> For *historical* reasons??
Because people have always done it that way, even though it conflicts
with the more natural (to programmers) way of 0-based indexing.
> * "there may be small differences between the two sequences, either
> because of errors during the sequence determination or because they
> are from different but related organisms"
> -> Or because they're paralogues, or alleles. (I just suggest relaxing the
> 'either...or' so it doesn't imply these are the two only reasons.)
> * As for the length of the article, I agree that the dp section can go;
> maybe just modify slightly the section on align() from "we'll look at this
> utility class later" into something like "which is also implemented in
> Perl". Conceivably even the section on subseqs could go, but IMHO it would
> be more rewarding to trim on the side of what points the article conveys.
> I'm just thinking about how many readers will react along the lines of "I
> know Perl is good at doing such projects, and the bio stuff confuses me.
> Other than claim that large projects can be done using such base classes,
> have you really found out that it works well and it doesn't get too
> sluggish as the project grows?"
Thanks for the helpful comments.
Lincoln D. Stein Cold Spring Harbor Laboratory
firstname.lastname@example.org Cold Spring Harbor, NY
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