These protein databases are used in the proteome browser. You don't need them
for
your specific genome.
You can read about how they were created in the source tree:
src/hg/makeDb/doc/proteins/*.txt
--Hiram
Jaysheel Bhavsar wrote:
> Thanks Hiram,
> This seems to work but what are the tables in the proteinsX db, I
> haven't been able to find any info on what each table holds.
>
> Thank you
> Jay
>
> On Apr 1, 2010, at 1:11 PM, Hiram Clawson wrote:
>
>> For a quick work-around since this isn't a genome that actually needs this
>> particular database, try simply creating an empty database:
>>
>> $ hgsql -e "create database proteins040315;" mysql
>>
>> If that doesn't work, download the actual protein databases, from, for
>> example:
>> ftp://hgdownload.cse.ucsc.edu/mysql/proteins040315/
>> or text dumps:
>> ftp://hgdownload.cse.ucsc.edu/goldenPath/proteinDB/proteins040315/database/
>> or rsync
>> rsync -avz --progress rsync://hgdownload.cse.ucsc.edu/mysql/proteins/040315/
>> or
>> sync -avz --progress
>> rsync://hgdownload.cse.ucsc.edu/goldenPath/proteinDB/proteins040315/database/
>>
>> It may need the other protein databases too.
>>
>> --Hiram
>>
>> Jaysheel Bhavsar wrote:
>>> 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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