[Genome] [BULK] Re: uncertain annotations in UCSC

[Na Liu]

Hi, Angie,

I logged in Giri. I obtain such a file :  
repeatmaskerlibraries-20071204.tar.gz

the procedure for obtaining it is:
1. I click the link :  http://www.girinst.org/repbase/update/index.html
2. at the bottom of this page, I noticed the Drosophila. Then I click  
the drorep.ref.  Then I downloaded the above file  
(repeatmaskerlibraries-20071204.tar.gz)
3. When I search 'FB4' in the file, I found there was only one  
FB4_DM.  How do you get the results listed in UCSC? (According to my  
calculation, there are totally 389 entries annotated as FB4_DM. How  
did you get the 389 entries? What criteria did you use to annotate is  
as FB4_DM? )


Look forward to your reply   and Have a good weekend.

Na


On Mar 7, 2008, at 1:06 PM, Angie Hinrichs wrote:

> Hi Na,
>
> UCSC does not assign the names; we simply run RepeatMasker on the
> genome and display its results.  RepeatMasker works by aligning
> consensus sequences from a library file to the genome.  The library
> file is the source of the repeat name, class and family annotated by
> RepeatMasker.  The library file is owned by RepBase Update (GIRI), but
> can be viewed after completing a registration process.  To retrieve
> the library file, visit this web page:
>
> http://www.girinst.org/repbase/index.html
>
> On the left there is a "Free registration" link.  After you have
> completed the registration process, the information in RepBase Update
> and/or RepBase Reports may be helpful.
>
> Best wishes for your research,
> Angie
>
>
> On Fri, 7 Mar 2008, Na Liu wrote:
>
>> Dear professors,
>>
>> I want to obtain all FB elements information of Drosophila
>> melanogaster  from UCSC. I am not sure if my extracting way is
>> correct because the results are suspectable:
>>
>> firstly , I choose 'Variation and Repeats ' in the group box by
>> using   TableBrowser.  Below, at the output format box, I choose "all
>> fields from selected table".
>>
>> Then I obtained a long list.  I notice there are some entries
>> annotated as FB4_DM. Are they meant FB elements? Why do you name them
>> FB4, not FB?  What do you mean by the number '4'?  They are
>> suspectable because some of them are very short (may be ~30nt, 40nt,
>> 50nt,....)and can not form a hairpin structure(according to the
>> definition, FB element has long inverted terminal repeats).
>>
>> If my extracting method is not correct, could you please tell me the
>> correct one?
>>
>> Look forward to your reply
>> sincerely .!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> Look forward to your reply
>> sincerely .!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>> Look forward to your reply
>> sincerely .!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>>
>> Best
>> Na
>>
>>
>>
>>       
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