Hello Carsten
Normally you would be able to use the Table browser to download any of
the source tables, but Genbank data is very large. So our recommendation
is to use the Table browser to learn about the tables/schema, then
actually obtain the data from the downloads server.
mysql_table_name == downloads_file_name.txt.gz
Table browser navigation:
1) Navigate to assembly (hg18) and the track (Human mRna)
2) Leave the default primary table, then click on "describe table schema"
3) The schema page has the primary table defined and associated tables
listed. Click on any of these associated tables brings them to the top
section so that their schema is defined. This can help you to choose the
data you want and to understand the linkage for any track, if you are
accessing more than one table/file.
4) for you case, click on the associated table "gbCdnaInfo"
5) in the new list of tables, click on the associated table "cds". This
table contains any information about the cds contained in the original
Genbank submission report ('data sheet").
Next, navigate the downloads server to understand where the file(s) you
are interest in are located. Starting at:
http://genome.ucsc.edu ->
left side-bar link "Downloads"
http://hgdownload.cse.ucsc.edu/downloads.html ->
common name link "Human"
http://hgdownload.cse.ucsc.edu/downloads.html#human ->
scroll down to "Mar. 2006 (hg18)"
and the 3rd link down "Annotation database" ->
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/
The README explains how to ftp/rsync to:
goldenPath/hg18/database/<file_name>
You will need to filter the files after downloaded, to limit the data to
that contained in the mRna track. Use the IDs in the track's primary
table all_mrna to pull out rows from cds with the same sequence name.
Hopefully this is helpful! Please feel welcomed to ask any new or follow
up questions to the mailing list at [email protected]
Regards,
Jen
On 6/30/10 9:05 AM, Carsten Raabe wrote:
> To whom it may concern,
> I am searching for a particular piece of information. I would like know
> whether it is possible to download preexisting the CDS annotations for
> the human all_mRNA dataset (>>> 2006 release). I would like to know
> where within the mRNA the CDS starts and where translation stops. Is
> there any way to get this information presumably via the table browser ?
>
> Thanks a lot in advance,
>
> Carsten
>
> PS any kind of table will do!
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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