Bioperl-guts: Re: Bio::Seq feedback

[Andrew Dalke]

Kate <katel@worldpath.net> 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.

By example,
 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] )



						Andrew Dalke
						dalke@bioreason.com
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