[ensembl-dev] Is there an is_circular flag stored somewhere for sequences

Andreas Kahari ak at ebi.ac.uk
Wed Sep 15 09:33:36 BST 2010


This is true if you're using the HEAD revision of the Ensembl Core API
(which will become release 60 later), but the API code that supports
circular chromosomes is code which is under development and, from our
point of view, highly experimental.  It was added to support circular
chromosomes in Ensembl Genomes, but the merge of that code has not been
properly tested yet (only to make sure non-circular stuff won't break).

As far as I'm aware, no Ensembl species (e.g., human) uses circular
sequence regions yet.  It is not up to me to debate whether that is
biologically correct or not.

With kind regards,

On Wed, Sep 15, 2010 at 09:17:25AM +0100, Uma Maheswari wrote:
> Hi,
> The seq regions can be set to circular using attrib_type called
> circular_seq.  They are set in the table seq_region_attrib
> Uma
> Hervé Pagès wrote:attrib_type
> >Hi,
> >
> >I'm new to Ensembl and I've started to look at the db schema to see
> >if it stores the information I need for my project.
> >One thing I need to know is whether the sequences described in
> >the 'seq_region' table are circular or not.
> >For example, given its name (MT) I know that sequence with
> >seq_region_id 100965601 (from homo_sapiens 59) is circular but
> >I'm wondering if this information is actually stored somewhere.
> >I've been looking at many connected tables but with no success.
> >
> >Any hints would be highly appreciated. Thanks in advance!
> >
> >H.
> >
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom

More information about the Dev mailing list