Hi Hiram,
I am not sure if that is what need to be done hear, I am not yet
familiar with the browsers working. When it get to the "base" level of the
view, and click on a region of the bed file that I uploaded, I get the
following error message
Couldn't connect to database proteins040315 on xxxx.edu as yyyy. Unknown
database 'proteins040315'
(xxxx= host name, and yyyy=usename for mysql)
how are the proteinsX tables create? I understand that system is looking for
proteins040315 database because that is what 'default' points to in gdbPdb
table.
Does this help?
Thank you
Jay
On Apr 1, 2010, at 11:57 AM, Hiram Clawson wrote:
> Good Morning Jay:
>
> It isn't clear what you are referring to here.
>
> Do you say you have protein sequences that you want to load into the genome
> browser ?
>
> To do that, you need to align the proteins to the genome with an aligner,
> for example blat. Once you have those positions as psl files, you can load
> the psl file as a track in the genome browser.
>
> --Hiram
>
> Jaysheel Bhavsar wrote:
>> Hi guys,
>> I am very new at this genome viewer business, so please bare with me if
>> I don't have the terminology or understanding of the inner workings. I
>> need to get genome browser up and running for genome that we have in the
>> lab. I have been able to get a local copy of genome browser up and running,
>> and have been able to add a custom track, along with gc5Base, and wiggle
>> info as described here
>> (http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database).
>> Everything seem to work as expected (I haven't played around with all the
>> options in trackDb.ra, but that will come later).
>> Issue 1:
>> Now the issue is that I am not able to get to the actually proteins/seq
>> for the tracks loaded. From what I understand I can create an entry in
>> gdbPdb, which seems straight forward (insert statement with org db name like
>> hg18 and proteinsX name). But I can't see find information as to what needs
>> to be in proteinesX database. I wasn't able find a utility or hgX loader
>> script either (unless I missed it). Could someone please point me in the
>> right direction, as to how to upload my protein/seq data.
>> Issue 2:
>> I have some metadata associated with each chromosome that I loaded into
>> db, is there a way to show that info on the browser? I have a tab delimited
>> file of protein id, gotermId and go annotations.
>> Thank you Jay
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