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

[Jason Stajich]

> 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.

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

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu