[Bioperl-l] additional methods for Bio::SeqUtils for in-silico cloning

Peter Cock p.j.a.cock at googlemail.com
Thu Jan 19 06:04:06 EST 2012


On Wed, Jan 18, 2012 at 6:11 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> You could probably change "<1" to "<" if the start isn't meant to be defined;
> the former seems to imply the feature location is '1 or before the start', the
> latter is simply 'before the start'.  Either version should work within bioperl
> AFAIK, though I'm not sure whether the feature table definition covers '<N'
> as a location type.
>
> Just thinking aloud, but such behavior might be something that needs to
> be defined more specifically in the Bio::RangeI implementation, via trunc().
>
> chris

Using '<1' or in general '<N' for an integer N should be fine for GenBank/EMBL
feature tables - not sure about '<' though, can say I recall ever seeing that.

There are some similar issues with UniProt/SwissProt files and features.
There I've seen '<1' used for before start (a partial peptide), but they also
have '?' for unknown which has no analogue in the GenBank/EMBL feature
table.

Peter



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