[Genome] CpG islands prediction in a mouse sequence

[Archana Thakkapallayil]

Hello Daniel,

The CpG Islands track is now available on the Mouse Jul. 2007 assembly.

There are different ways to identify the CpG Islands in your region of 
interest.

1. Enter your position : chr4:147,410,917-147,415,735, into the 
position/search box on the mm9 browser. Then turn on the 'CpG Islands' 
track,  which is located under the group 'Expression and Regulation'. 
Clicking on the individual items on this track will take you to the page 
that contain the details about the CpG Island.

2. Another way to get this information is by using the Table Browser. To 
do this configure the Table Browser like so:

clade: Vertebrate
genome: Mouse
assembly: Jul. 2007
group: Expression and Regulation
track: CpG Islands
table: cpgIslandExt
region: select the 'position' radio button and then enter your position 
into the search box
choose your output type for download and then hit 'get output'.

I hope this information helps.  If you have further questions, please 
feel free to write back to this list.

Regards,

Archana
UCSC Genome Bioinformatics Group

Archana Thakkapallayil wrote:
> Hello Daniel,
>
> Currently, the Mouse Jul. 2007 Assembly does not contain the CpG Islands 
> track. We will be adding this track soon for the mm9 assembly. I will 
> let you know when it is available and give you the detailed instructions 
> on getting this information.
>
> Regards,
>
> Archana
> UCSC Genome Bioinformatics Group
>
>
> Daniel Leclerc wrote:
>   
>> Hello,
>>
>> I am trying to use the genome brower to identify CpG islands in a 
>> specific mouse genomic sequence.
>>
>> I am using the UCSC Genome Browser on Mouse Jul. 2007 Assembly.
>> The relevant DNA sequence is chr4:147,410,917-147,415,735.
>> I am using Internet Explorer 6.0, under Windows 2000.
>>
>> I would appreciate a kind of "step-by-step" list of instruction to 
>> make me able to get the prediction of CpG islands in this segment.
>>
>> Thank you,
>>
>> Daniel Leclerc
>>
>> **********************************************************
>> Dr Daniel Leclerc, Ph.D.
>> McGill University- Montreal Children's Hospital,
>> Research Institute (Place Toulon),
>> Medical Genetics - Room 242,
>> 4060 Ste-Catherine West,
>> Montreal, Canada
>> H3Z 2Z3
>> Phone: (514) 412-4400 x 23281
>> FAX:   (514) 412-4331
>> email: daniel.leclerc at mail.mcgill.ca
>> ********************************************************** 
>>
>> _______________________________________________
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>>   
>>     
>
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