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

[Heikki Lehvaslaiho]

On Wed, 2002-10-23 at 14:09, Lars G. T. Jorgensen wrote:
> 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.

Lars,

Like Jason said you really do not want to use Bio::LiveSeq unless you
want to change the sequence and keep track of those changes. 

However, it can read in nucleotide database entries and there is a
sample script showing how to do it here:

scripts/liveseq/change_gene.pl

EMBL/Genbank formats are not too well suited for collecting exon/intron
boundary information. If there are multiple transcripts and annotators
have not been consistant in labeling which exon belongs to which gene,
and you are in deep trouble.  

We do not yet have a usable set of classes for this. Your best bet is
Bio::SeqFeature::Gene::* name space.

Check also question 5.2 in the FAQ.

	-heikki

> > 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
> System administrator     | Student 
> Bioinformatics Centre    | Department of Computer Science  
> University of Copenhagen | University of Copenhagen
> http://www.binf.ku.dk    | http://www.diku.dk
> When's the last time you used duct tape on a duct? -- Larry Wall
> 
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-- 
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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