[Genome] EST sequences

[Brooke Rhead]

Hello Vidar,

To display ESTs from a particular library in the Genome Browser, first 
turn on the "Human ESTs" track (in the "mRNA and EST Tracks" section). 
Then go to the track control page, either by hitting the small button on 
the far left-hand side of the track, or by clicking the blue "Human 
ESTs" link right above the track control.  The track control page 
contains several options for filtering the data displayed in the EST 
track, one of which is "library".  Enter the library name of interest in 
the box.  You may need to add wildcard characters to the library names, 
as we store longer names than your example in our database.  For 
instance, the library name "2NbHMSP" used as a filter term yields no 
results, but the name "*2NbHMSP" matches these two libraries:

Soares 2NbHMSP
Soares_multiple_sclerosis_2NbHMSP

If you click on the EST in the Genome Browser, you will be taken to a 
details page, where there is a link to the EST sequence.

To get a lot of EST sequences at once, you will need to download the 
entire file of EST sequnces that we get from GenBank.  (The Table 
Browser can be used to retrieve genomic sequence from the areas where 
ESTs align, but the EST sequence itself is not stored in a table and is 
not available via the Table Browser.)  The file is located here:

http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/est.fa.gz

Be aware that this is a very large file (~1.4G).  The file is in FASTA 
format.

The Table Browser *could* be used to get a list of the EST accession 
numbers in a particular library, but due to the huge size of the all_est 
table and the complexity of the query, it is very time-consuming to use 
  it for this purpose.  It is much easier to use our public MySQL 
database to obtain the information:

http://genome.ucsc.edu/FAQ/FAQdownloads#download29

Here is an example MySQL query that will get you a list of accessions in 
  the second library listed above:

mysql> SELECT gbCdnaInfo.acc FROM gbCdnaInfo, library WHERE 
gbCdnaInfo.type='est' AND gbCdnaInfo.library=library.id AND 
library.name='Soares_multiple_sclerosis_2NbHMSP';

I hope this information is helpful.  If you have further questions, 
please feel free to contact this mailing list again.

-- 
Brooke Rhead
UCSC Genome Bioinformatics Group



Vidar Blikstad wrote:
> Hello!
> 
> I´m a user of the table browser - can you help me to obtain EST  
> sequences from a UniGene library (i.e.2NbHMSP). How to display these  
> at the genome browser?
> 
> Sincerely
> 
> Vidar Blikstad
> Uppsala university
> 
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome