Hello Jennifer. Thank you for fast response. I have been looking at the
options you gave me and I feel I am a bit feather, though not quite there
yet.
1) Table browser option. The human net track seams to align all the human
genome with lab mouse homologous nucleic sequences. After selecting that
table I got 279 MB tab separated file with thease headers:
#bin score tName tSize tStart tEnd qName qSize qStrand qStart qEnd id
I can guess what are some of the columns, though is there any description
for those names so for me to be sure I got it right?
Having the nucleic genome aligned how can I extract only protein coding
regions that correspond to the genes that interest me? (at the end I only
need aligned mouse and human protein sequences of the genes that correspond
to DNA repair, let's say those from gene ontology database that show up
after the search on terms "DNA"+"repair" on human genome).
2) MySQL option. I got connected to the public server and I found a lot of
databases and tables, though I didn't find any ER diagrams and field
description on the site. What databases should I look at and where to find
field description?
Greetings,
Hernando Sanchez
On Fri, Apr 16, 2010 at 7:20 PM, Jennifer Jackson <[email protected]> wrote:
> Hello Hernando,
>
> There are a few options for you:
>
> 1) Use the Table browser for the batch query, possibly in combination with
> Galaxy to perform full intersections. The intermediate mapping tables could
> be the Conservation track or the Chain/Net tracks between Human and Mouse.
>
> 2) Download the text files representing the tables in the database for the
> datasets in #1, then create scripts to process your query. Tools from the
> UCSC utility set may be helpful.
>
> 3) Use the public mySQL server to gain directly access to the database and
> use mySQL, utilities from our source tree, your own tools, etc. to process
> the query.
>
> 4) Create a local mirror of the Browser and do the same as #3, but locally
> in your own instance.
>
> Do you have a preference? #4 would be the most private option, if that is a
> concern for you, but would require the most up-front work and may not be
> necessary.
>
> Please write back and let us know your preference and we can send full
> details about suggested tables & utilities, file download/ftp help, and
> mirroring assistance.
>
> Thank you,
> Jennifer
>
> ---------------------------------
> Jennifer Jackson
> UCSC Genome Informatics Group
> http://genome.ucsc.edu/
>
>
> On 4/16/10 8:10 AM, Ernando Faddeev wrote:
>
>> I want to compile a list of conserved protein coding transcripts(/genes)
>> between mouse (mm9<http://genome.ucsc.edu/cgi-bin/hgGateway?db=mm9>) and
>>
>> human(hg19) that are involved with DNA repair. Basically I want the table
>> with names next to aligned sequences of the transcripts. I have the names
>> and accession numbers of around 300 human genes that I am interested in,
>> and
>> now I want to find the sequences of their mouse homologous. GBrowser
>> appears
>> to do so in some extend, though only gene by gene and graphically. I have
>> the required computational skills required to install the database and
>> manage scripts, though I do not know where to start and what tools to use,
>> so therefor the question: what tools can I use to build this DB?
>>
>> Greetings,
>> Hernando Sanchez
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>>
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
