[BioSQL-l] circular

[mark.schreiber at novartis.com]

So 'is_circular' should be the blessed term. It really needs to be a 
convention so that reading and writing is consistent between bio* 
projects.

Would it be a good idea for the sequence table of BioSQL 1.1 to have a 
circular column?

- Mark





"Marc Logghe" <Marc.Logghe at devgen.com>
06/20/2005 05:33 PM

 
        To:     Mark Schreiber/GP/Novartis at PH, <biosql-l at open-bio.org>
        cc: 
        Subject:        RE: [BioSQL-l] circular


Hi Mark,
As far as I am aware of, there is currently no field available in the
bioentry table to store that kind of flag.
It is parsed out from genbank files by BioPerl, though.
It is taken from the genbank Locus line, eg.
"LOCUS       BBPLAS                  2687 bp    DNA     circular BCT
12-MAR-1999"
You can check the resulting Bio::Seq::RichSeq object by running the
is_circular() method from Bio::PrimarySeq.
A solution would be to make a Bio::Factory::SequenceProcessorI compliant
processor and pass that as an option to your load_seqdatabase.pl script.
In the procesor itself, you can for instance do the following:
1) check for circularity using the is_circular() method
2) if circular, add a term to your sequence object (eg. annotation term,
gene ontology term 'is_circular') indicating it is circular

My 0.02$

Cheers,
Marc


> -----Original Message-----
> From: biosql-l-bounces at portal.open-bio.org 
> [mailto:biosql-l-bounces at portal.open-bio.org] On Behalf Of 
> mark.schreiber at novartis.com
> Sent: Monday, June 20, 2005 7:34 AM
> To: biosql-l at open-bio.org
> Subject: [BioSQL-l] circular
> 
> Hello -
> 
> When circular sequences (plasmids, bacterial genomes etc) are 
> stored in BioSQL how is their circularity indicated? Or, what 
> should the convention be?
> 
> - Mark
> 
> Mark Schreiber
> Principal Scientist (Bioinformatics)
> 
> Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road
> #05-01 Chromos
> Singapore 138670
> www.nitd.novartis.com
> 
> phone +65 6722 2973
> fax  +65 6722 2910
> 
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