[Genome] a question for ucsc

[Archana Thakkapallayil]

Hello again Barak,

You could also get this information by clicking on to the details of 
individual EST and from this page click on the link to the base-level  
"EST/Genomic Alignments".

Regards,
Archana.

Archana Thakkapallayil wrote:
> Hello Barak Mizrahi,
>
> Unfortunately, we don't have any tables that store the exact locations 
> of mismatch between the EST and the DNA. However you could view this on 
> the Browser, by turning on the 'Human ESTs' track to full visibility and 
> then zoom in to the base level. Now click on to the track settings page 
> by clicking on the vertical blue-or-grey bar on the left hand side of 
> this track. Then choose "different mRNA bases" from the 'Color track by 
> bases' pull down menu and then click the 'submit' button. You can see 
> the mRNA bases that differ between the genome and the EST are printed on 
> the browser.
>
> Also, the Genome Browser offers several ways to highlight gaps in 
> alignments of query sequences (usually transcripts) to the genome. 
> Alignment gaps result from sequence in the genome or query (or both) 
> that cannot be aligned, usually due to a deletion in one sequence or an 
> insertion in one or both sequences. You can view this on the browser by 
> checking the boxes under "Alignment Gap/Insertion Display Options" on 
> the track settings page. More information about this feature is here:
> http://genome.cse.ucsc.edu/goldenPath/help/hgIndelDisplay.html
>
> I hope this information is helpful to you. If this does not answer your question, please don't hesitate to write back to the list.
>
> Regards,
>
> Archana
> UCSC Genome Bioinformatics Group
>
> We invite you to give us your feedback on the UCSC Genome Browser through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177
>
>  
>
> Barak Mizrahi wrote:
>   
>> hello, 
>>  
>> I am using the ucsc for academic research ,
>>  
>> how can I find in EST  the location of a mismatch , 
>> I saw for example in ALL_EST table with a summary of the compare between est and dna but if I want to know the exact location of each insert delete update where can I find it ? 
>>  
>> tx
>>
>>
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>>   
>>     
>
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