[Genome] uncertain annotations in UCSC

[Angie Hinrichs]

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
> 
> 
>  
>      =====================================================================
>      
>      Please note that this e-mail and any files transmitted with it may be 
>      privileged, confidential, and protected from disclosure under 
>      applicable law. If the reader of this message is not the intended 
>      recipient, or an employee or agent responsible for delivering this 
>      message to the intended recipient, you are hereby notified that any 
>      reading, dissemination, distribution, copying, or other use of this 
>      communication or any of its attachments is strictly prohibited.  If 
>      you have received this communication in error, please notify the 
>      sender immediately by replying to this message and deleting this 
>      message, any attachments, and all copies and backups from your 
>      computer.
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome