[Bioperl-l] Re: [Root-l] new Bioperl bug tracking system

[Lars G. T. Jorgensen]

Jason Stajich <jason@cgt.mc.duke.edu> writes:

> > Ok, whats a "live" sequence and what is a "rich" sequence. Is the
> > latter just a sequence taken from a database?
> 
>  This is "our" jargon not biological jargon.  A Live seq - I assume you
> mean seqs in Bio::LiveSeq::SeqI?  This is a separate class of
> implementations meant to handle sequences which are being mutated with
> insertions and deletions.  Heikki can explain all the historical nuances
> but suffice to say you don't need to use these unless you are trying to
> represent the same sequence before and after a mutation.

I was doing a project where I needed to represent genomic DNA
sequences and know the index of the introns (and/or) exons. Is this
the kind of sequence i should use and is there someway of transforming
a RichSeq object into a LiveSeq object.

> 
> RichSeq represent is for sequences which come out of richly annotated
> sequence files (Genbank,EMBL,SwissProt).  These have extra methods for
> pid, secondary_accessions, keywords, dates, sequence versions, etc.
> 
> ...from the docs of Bio::Seq::RichSeqI...
> =head1 DESCRIPTION
> 
> This interface extends the Bio::SeqI interface to give additional
> functionality to sequences with richer data sources, in particular from
> database sequences (EMBL, GenBank and Swissprot).
> ...
> 
> 
> If you parse a genbank/embl file with SeqIO you will get a
> Bio::Seq::RichSeqI object back (unless you tell SeqIO you want PrimarySeq
> or Seq objects instead).
> 
> -jason

-- 
Mvh|Regards, Lars
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