[ensembl-dev] CpG Island

[Yuan Chen]

Thanks both. Great help :)

yuan
On 11 Jan 2012, at 14:29, Susan Fairley wrote:

> Hi Yuan,
> 
> The process by which the score is generated is similar to the one described below although, as Bert mentioned, the minimum length requirement is 400bp. I believe the score reported is the maximum score reached for the island.
> 
> From https://lists.soe.ucsc.edu/pipermail/genome/2004-July/005149.html:
> "Instead of a sliding-window search for CpG islands, this cpg program
> uses a running-sum score where a 'C' followed by a 'G' increases the
> score by 17 and anything else decreases the score by 1.  When the
> score transitions from positive to 0 (and at the end of the sequence),
> the sequence in the current span is evaluated to see if it qualifies
> as a CpG island (>200 bp length, >50% GC, >0.6 ratio of observed CpG
> to expected)."
> 
> I hope that helps.
> 
> Regards,
> Susan.
> 
> Bert Overduin wrote:
>> Yuan,
>> Also note that for human Ensembl uses for CpG islands a cut-off of 400
>> bp. Smaller CpG islands are not stored.
>> Cheers,
>> Bert
>> On Wed, Jan 11, 2012 at 9:41 AM, Yuan Chen <yuan at sanger.ac.uk> wrote:
>>> Thank very much, Susan.
>>> 
>>> In the simple_feature table for cpg, there is score column, the maximum score is 34968 and minimum score is 37, do you know the meaning of this score ?
>>> 
>>> yuan
>>> On 11 Jan 2012, at 09:28, Susan Fairley wrote:
>>> 
>>>> Hi Yuan,
>>>> 
>>>> The CpG islands are stored as simple features in the human core database. Their analysis has the logic_name cpg.
>>>> 
>>>> homo_sapiens_core_65_37 >select logic_name , count(*) from analysis, simple_feature where analysis.analysis_id =simple_feature.analysis_id group by logic_name ;
>>>> +------------+----------+
>>>> | logic_name | count(*) |
>>>> +------------+----------+
>>>> | cpg        |    23511 |
>>>> | eponine    |    62774 |
>>>> | firstef    |    89002 |
>>>> | trnascan   |      834 |
>>>> +------------+----------+
>>>> 4 rows in set (0.36 sec)
>>>> 
>>>> Kind regards,
>>>> Susan.
>>>> 
>>>> Yuan Chen wrote:
>>>>> Hi All,
>>>>> Do ENSEMBL have CpG island data on human available some where ?  Cheers
>>>>> yuan
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