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

[Hervé Pagès]

Hi Uma, Andreas,

Thanks for your answers. I'm not planning to use the Ensembl Core API
for this. Just to download table dumps.

So to summarize, yes the current schema would allow support for this
(thru attrib type circular_seq) but this attrib type is currently not
used in Ensembl (and indeed I don't see it in the 'attrib_type' table).
Are there any plans to add it to release 60?

Thanks again for your help.

Cheers,
H.


On 09/15/2010 01:33 AM, Andreas Kahari wrote:
> Hi,
>
> 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,
> Andreas
>
> 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.
>>>
>>
>>
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>>
>


-- 
Hervé Pagès

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