Bioperl-guts: Re: Bio::Seq feedback
Mon, 02 Aug 1999 14:42:39 -0600
Kate <firstname.lastname@example.org> said:
> You'd get different translations, from RNA to protein, depending
> on where you start. You might want to try start 0, 1, 2 and see
> which matches a protein sequence.
Hmm, I thought "start" meant something different than that.
I thought it meant the given sequence was really a subsequence of
a larger sequence, and "start" indicates the position of the
first base in the subsequence with respect to the larger one.
x = ATTATACGTAGC
y = TATA
let x.start == 1
and let y = x[3rd base to 6th base, inclusive] == "TATA"
then y.start should be 3.
This seems to be the meaning given in http://bio.perl.org/Core/POD/Seq.html
I also thought that the start offset used for translation would be a
function of the translation code, as in
protein = translate(rna, 0) # or rna.translate, if you prefer
or since you can get the protein sequence without the first character
protein translate( rna[first character through end] )
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